CDC cooperative agreements involve a unique combination of scientific collaboration, federal compliance requirements, and programmatic accountability. After observing patterns across health departments managing CDC-funded programs, certain mistakes appear repeatedly. These are not edge cases — they are predictable, preventable failures that cost organizations time, credibility, and sometimes funding. This guide documents the most common mistakes, explains why they happen, and provides specific corrective actions for each.
Mistake #1: Late or Incomplete Continuation Applications
The problem: Continuation applications for Years 2 through 5 are submitted late, incomplete, or with insufficient detail. This is the single most common operational failure in CDC cooperative agreement management, and it has immediate financial consequences.
Why it happens: Continuation applications are due 90 to 120 days before the start of the next budget period — while you are still in the middle of the current year's work. The deadline often falls during peak program activity. Staff who are managing active surveillance programs, responding to disease outbreaks, or coordinating community interventions view continuation applications as administrative paperwork competing with urgent programmatic needs.
The consequences: Late continuation applications delay the issuance of the continuation award. Until the award is issued, your organization may need to pre-fund activities from other sources or halt spending entirely. For state health departments managing 5 to 10 CDC cooperative agreements, late continuations across multiple awards can create significant cash flow problems. In extreme cases, CDC may reduce the continuation amount or shorten the budget period.
How to Prevent It
- Build a master continuation calendar: Maintain a single calendar showing continuation application due dates for every CDC cooperative agreement. Set internal deadlines 30 days before the CDC deadline to allow time for review and revisions.
- Assign dedicated staff: Do not assume the program director will handle the continuation application on top of their program management duties. Assign a grants management specialist or coordinator to track deadlines and coordinate submission components.
- Draft the work plan throughout the year: Do not start the next year's work plan from scratch when the continuation application is due. Maintain a running document that captures lessons learned, needed modifications, and planned activities as they emerge during the current budget period.
- Engage your PO early: Discuss continuation plans with your CDC project officer at least 3 months before the application is due. The PO can flag areas needing attention, suggest work plan modifications, and confirm budget expectations.
Mistake #2: Not Engaging the CDC Project Officer Early and Often
The problem: Recipients treat CDC cooperative agreements like grants — receiving the award and then operating independently, contacting the project officer only when submitting required reports or encountering a crisis. This fundamentally misunderstands the cooperative agreement model.
Why it matters: The "substantial involvement" provision exists because CDC intends to be an active partner, not a passive funder. Project officers have access to national data, cross-site perspectives, emerging best practices, and T/TA resources that can significantly improve your program's effectiveness. When you do not engage your PO, you are leaving value on the table — and you are also missing early warning signals about performance concerns that could affect your continuation funding.
How to Prevent It
- Schedule regular check-ins: Establish monthly or quarterly calls with your CDC project officer. Use these calls to share progress, discuss challenges, and ask for guidance. Do not wait for problems to escalate.
- Share challenges proactively: If you are falling behind on a work plan milestone, experiencing staffing gaps, or encountering unexpected barriers, tell your PO sooner rather than later. POs can often help troubleshoot or adjust expectations if informed early. Surprises in the annual performance report are never welcome.
- Invite PO participation: Include your project officer in relevant meetings, share data summaries, and ask for their input on strategic decisions. The best cooperative agreement relationships function as genuine collaborations.
- Attend grantee meetings prepared: Come to annual grantee meetings with specific questions, challenges to discuss, and results to share. Use the face-to-face time to build the relationship.
Mistake #3: Rebudgeting Without Prior Approval
The problem: Recipients transfer funds between budget categories without tracking cumulative transfers, exceeding the 25% prior approval threshold without obtaining written authorization from the Grants Management Specialist (GMS). This is a serious compliance violation under 45 CFR Part 75.
Why it happens: Budget reallocation often happens gradually. A vacancy savings in personnel gets shifted to contractual. Travel costs come in higher than budgeted. Supply costs increase due to a public health response. Each individual transfer seems small, but cumulative transfers over the budget period can easily exceed 25% without anyone tracking the aggregate.
How to Prevent It
- Track cumulative transfers continuously: Maintain a running budget-to-actual comparison for each CDC award that shows cumulative transfers between categories as a percentage of the total budget. Review this monthly. See the Budget guide for rebudgeting threshold details.
- Set internal alert thresholds: Establish an internal policy that triggers a review at 15% cumulative transfer — well before the 25% threshold. This gives you time to prepare a prior approval request if the trend will continue.
- Submit prior approval requests proactively: If you know you will exceed 25%, submit the prior approval request to the GMS before making the transfer. Include the revised SF-424A, a clear explanation of why the rebudgeting is needed, and how it supports program objectives.
Mistake #4: Publishing Without CDC Clearance
The problem: Recipients publish journal articles, present at conferences, distribute educational materials, or post website content that references CDC-funded work without obtaining CDC clearance first. This violates CDC standard terms and conditions and can create significant problems.
Why it happens: Academic partners and program staff accustomed to other funding mechanisms do not realize that cooperative agreements have different publication requirements than standard grants. Journal submission deadlines and conference abstract deadlines create time pressure that leads staff to skip the clearance step. Some staff are not even aware that the requirement exists.
How to Prevent It
- Establish an internal clearance process: Create a policy requiring all CDC-funded publications, presentations, and materials to go through an internal review before submission to CDC for clearance. This filters out issues before they reach CDC.
- Plan for clearance timelines: CDC clearance can take 30 to 90 days. Factor this into your publication and presentation timeline. If submitting a journal article, begin the CDC clearance process before finalizing the manuscript for submission.
- Train all staff and partners: Ensure that every staff member, sub-recipient, and academic partner working on the cooperative agreement understands the publication clearance requirement. Include it in sub-award agreements and in onboarding materials for new staff.
- Include acknowledgment language: Verify that the required CDC acknowledgment and disclaimer language is included in every publication. See the Compliance guide for the standard language.
Mistake #5: Weak Evaluation Plans
The problem: Recipients develop evaluation plans that describe data collection activities but do not constitute genuine evaluation. Plans focus on counting outputs (number of trainings conducted, number of people tested) rather than measuring outcomes (changes in health behaviors, reductions in disease incidence, improvements in systems capacity).
Why it matters: CDC has significantly increased its emphasis on rigorous program evaluation across all cooperative agreement programs. Evaluation plans are now scored in competitive applications, and evaluation findings are reviewed as part of continuation decisions. A weak evaluation plan signals to CDC that your organization does not have the capacity to learn from its work and improve over time.
How to Prevent It
- Hire or contract evaluation expertise: If your staff lacks evaluation training, budget for an evaluator (internal or contracted) who can design rigorous evaluation methods, analyze data, and produce meaningful findings.
- Use CDC's evaluation framework: CDC publishes evaluation guidance including the Framework for Program Evaluation in Public Health. Use this framework to structure your evaluation plan around stakeholder engagement, logic models, credible evidence, and justified conclusions.
- Distinguish outputs from outcomes: In your evaluation plan, clearly separate process evaluation (did we do what we planned?) from outcome evaluation (did what we did make a difference?). Both are important, but CDC wants to see evidence of impact, not just activity.
- Plan for data use: Describe how evaluation findings will be used to modify the program, inform stakeholders, and contribute to the evidence base. An evaluation that produces a report no one reads is not meeting CDC's expectations.
Mistake #6: Inadequate Sub-Recipient Monitoring
The problem: State health departments that sub-award CDC cooperative agreement funds to local health departments, CBOs, or universities fail to implement adequate monitoring of those sub-recipients. This is one of the most common Single Audit findings for pass-through entities.
Why it happens: Monitoring sub-recipients requires staff time, travel, and expertise that is often under-budgeted. Program staff focused on their own work plan activities view sub-recipient monitoring as an administrative burden. Some organizations lack written monitoring procedures entirely, relying on informal communication rather than structured oversight.
How to Prevent It
- Develop written monitoring procedures: Document your sub-recipient monitoring process including risk assessment methodology, monitoring frequency, review checklists, site visit protocols, and corrective action procedures.
- Conduct risk assessments: Assess each sub-recipient's risk level annually and calibrate your monitoring intensity accordingly. High-risk sub-recipients (new organizations, prior findings, large dollar amounts) need more frequent and intensive monitoring.
- Budget for monitoring activities: Include staff time, travel, and any monitoring tools in your CDC cooperative agreement budget. Sub-recipient monitoring is an allowable and expected cost.
- Review Single Audit reports: For sub-recipients expending $750,000+ in federal awards, obtain and review their Single Audit reports. Follow up on any findings related to your sub-award within 6 months of the audit report issuance.
Mistake #7: Poor Work Plan Alignment with NOFO Strategies
The problem: Work plans describe activities that the organization wants to do rather than activities that directly map to the NOFO's required strategies and objectives. This disconnect becomes apparent during annual performance reporting when accomplishments do not align with what CDC expected.
Why it happens: Organizations have existing programs and staff, and they naturally want to continue doing what they have always done. When a new NOFO shifts priorities or introduces new strategies, organizations sometimes force-fit their existing activities into the new framework rather than genuinely redesigning their approach to match NOFO requirements.
How to Prevent It
- Create a crosswalk: Build a table that maps each NOFO strategy to specific work plan activities, assigned staff, and measurable deliverables. If any NOFO strategy has no corresponding work plan activity, you have a gap. If any work plan activity does not map to a NOFO strategy, it may not be fundable.
- Review with your PO before finalizing: Share your draft work plan with your CDC project officer before submitting the continuation application. The PO can identify alignment issues and suggest modifications while there is still time to adjust.
Mistake #8: Equipment Purchases Without Prior Approval
The problem: Recipients purchase equipment costing $5,000 or more without obtaining prior written approval from CDC, even when the equipment was included in the approved budget. Under CDC standard terms and conditions, equipment purchases require prior approval regardless of whether they appear in the approved budget.
How to Prevent It
- Implement a purchase approval workflow: Require all purchases of $5,000 or more to go through a centralized review that verifies whether prior federal approval is needed before the purchase order is issued.
- Submit requests early: Equipment prior approval requests can take 4 to 8 weeks to process. Submit requests well in advance of when you need the equipment.
- Track equipment throughout the award: Maintain an equipment inventory for all items purchased with CDC funds, including location, condition, and usage. This information is required at close-out.
Mistake #9: Failure to Report Program Income
The problem: Income generated by CDC-funded activities — including fees, reimbursements from third-party payers, or interest earned on federal advances — is not identified, tracked, or reported as program income. Under 45 CFR Part 75, program income must be reported on the SF-425 and used for allowable program activities.
How to Prevent It
- Identify potential program income sources: At the start of each budget period, review whether any CDC-funded activities could generate income. Common sources include laboratory fees, clinical service reimbursements, and training fees.
- Configure your accounting system: Set up your financial system to capture program income separately, linked to the specific CDC award that generated it. Program income should be easily identifiable for SF-425 reporting.
- Report on every SF-425: Include program income on each quarterly or annual SF-425, even if the amount is zero. Consistent reporting demonstrates awareness of the requirement and prevents questions during audits.
Mistake #10: Not Understanding the Difference Between Sub-Awards and Contracts
The problem: Recipients misclassify the relationship with downstream entities, treating sub-recipients as contractors or vice versa. This misclassification has cascading compliance consequences — the wrong federal requirements are applied, audit implications are misunderstood, and monitoring obligations are not met.
How to Prevent It
- Apply the substance test: Use the criteria in 45 CFR 75.351 (equivalent to 2 CFR 200.331) to evaluate the substance of each relationship. Does the entity carry out part of the federal program, or does it provide goods and services for the recipient's use? The answer determines the classification.
- Document the determination: For each downstream relationship, document the analysis that led to the sub-recipient or contractor classification. This documentation is evidence of compliance during audits and monitoring visits.
- Consult the eligibility guide: The Eligibility page of this guide includes a detailed comparison table of sub-recipient vs. contractor characteristics to support your determination.
Building a Compliance-First Culture for CDC Awards
The common thread across these mistakes is a disconnect between compliance requirements and daily operations. Organizations that manage CDC cooperative agreements successfully do not treat compliance as a separate administrative function — they embed compliance awareness into program management, financial operations, and leadership decision-making.
Start by ensuring that everyone involved in CDC-funded work understands the unique features of cooperative agreements: substantial involvement, prior approval requirements, publication clearance, and the collaborative relationship with the project officer. Then build systems — calendars, workflows, checklists, and review processes — that make compliance the default rather than an afterthought. The goal is not to create more paperwork but to prevent the costly surprises that come from missing requirements that were foreseeable and preventable.