CDC Cooperative Agreements Guide for Health Departments

What Are CDC Cooperative Agreements?

CDC cooperative agreements are the primary funding mechanism through which the Centers for Disease Control and Prevention (CDC) supports public health infrastructure, disease prevention, and health promotion activities at state, local, tribal, and territorial levels. Unlike standard federal grants where recipients operate independently, cooperative agreements involve "substantial CDC involvement" in program activities — a legal distinction defined under 31 U.S.C. 6305 that shapes how recipients plan, execute, and report on funded work.

CDC distributes approximately $8 billion annually in extramural funding across more than 300 active Notices of Funding Opportunities (NOFOs). These funds support the backbone of public health in the United States: disease surveillance, laboratory capacity, immunization programs, emergency preparedness, chronic disease prevention, HIV/AIDS and STD prevention, environmental health, injury prevention, birth defects surveillance, and workforce development. For most state and local health departments, CDC cooperative agreements represent the largest single source of federal public health funding.

How Cooperative Agreements Differ from Grants

The distinction between a cooperative agreement and a grant is not merely administrative — it fundamentally shapes the recipient's relationship with CDC and the day-to-day management of the funded program. Understanding this difference is essential for anyone managing CDC funding.

In practice, the substantial involvement provision means that your CDC project officer is not just a monitor — they are a collaborator. They participate in planning meetings, review deliverables before finalization, provide scientific and technical guidance, coordinate cross-site activities, and ensure alignment with CDC's public health priorities. This collaborative relationship is both the greatest strength and the most misunderstood aspect of CDC cooperative agreements.

Major CDC Program Areas

CDC's organizational structure maps directly to its funding streams. Each center or division within CDC administers its own set of cooperative agreements, each with program-specific requirements layered on top of agency-wide compliance standards. Understanding this structure helps recipients navigate the landscape of available funding and the unique requirements of each program area.

• Epidemiology and Laboratory Capacity (ELC) — CFDA 93.323: One of the largest CDC programs, funding state and local epidemiology, laboratory capacity, and disease surveillance infrastructure. Annual awards range from $2M to $50M+ depending on jurisdiction size and supplemental funding.
• Public Health Emergency Preparedness (PHEP) — CFDA 93.069: Funds state and local preparedness for public health emergencies including bioterrorism, infectious disease outbreaks, and natural disasters. Awards are formula-based with a minimum allocation per jurisdiction.
• HIV/AIDS Prevention — CFDA 93.945: Supports HIV prevention activities including testing, PrEP access, partner services, and surveillance. Funding flows through PS20-2010 and related NOFOs to state and local health departments, CBOs, and tribal organizations.
• Immunization CoAgs — CFDA 93.268: The backbone of state and local immunization programs, funding vaccine distribution, coverage assessments, immunization information systems (IIS), and outbreak response. Every state and territory receives immunization cooperative agreement funding.
• Chronic Disease Prevention — CFDA 93.735: State Public Health Actions to Prevent and Control Diabetes, Heart Disease, Obesity, and Associated Risk Factors. Funds comprehensive chronic disease prevention strategies including tobacco cessation, nutrition, and physical activity interventions.
• STD Prevention — CFDA 93.977: Supports STD surveillance, partner services, screening programs, and outbreak investigation at state and local levels. Typically combined with HIV prevention infrastructure at the recipient level.
• TB Elimination — CFDA 93.116: Funds tuberculosis prevention and control including case management, contact investigations, directly observed therapy (DOT), and laboratory services.
• Environmental Health — CFDA 93.070: Supports environmental public health tracking, lead poisoning prevention, climate and health adaptation, and safe water programs.

The 5-Year Competitive Cycle

Most CDC cooperative agreements follow a 5-year project period with a defined competitive cycle. Understanding this cycle is critical for planning, staffing, and sustaining programs across award periods.

• Year 1 — Competitive application: CDC publishes a NOFO on Grants.gov with a detailed scope of work, eligible applicant types, scoring criteria, and funding levels. Applications are reviewed by a peer review panel and scored against published criteria. Awards are typically made within 60 to 90 days of the application deadline.
• Years 2–5 — Annual continuation: Each year, recipients submit a non-competing continuation application that includes an updated work plan, budget, performance narrative, and key personnel changes. Continuation funding is not guaranteed — it depends on satisfactory performance, availability of appropriations, and compliance with award terms.
• End of project period: CDC either recompetes the program through a new NOFO or discontinues the funding line. Recipients must plan for the transition, including close-out reporting, data transfer, and workforce implications.
• No-cost extensions: Recipients may request a 12-month no-cost extension (NCE) to complete activities and expend remaining funds. NCEs require justification and CDC approval.

The Role of the CDC Project Officer

The CDC project officer (PO) is the single most important contact you will have at CDC. Unlike grants officers in other agencies who focus primarily on administrative oversight, the CDC project officer is a subject matter expert who is deeply involved in your program's scientific and operational direction. The PO's role under the substantial involvement provision includes:

• Reviewing and approving annual work plans and evaluation plans
• Providing ongoing scientific and technical assistance
• Coordinating cross-site activities and peer learning among recipients
• Reviewing publications and presentations for scientific accuracy and CDC clearance
• Monitoring progress toward objectives and flagging concerns early
• Facilitating connections to other CDC resources and national experts

Building a strong, proactive relationship with your CDC project officer is among the most important things you can do. Recipients who engage their PO early and often avoid surprises, get faster resolution of issues, and benefit from the full value of the cooperative agreement model. See the Common Mistakes guide for detailed guidance on this topic.

Who This Guide Is For

This CDC Cooperative Agreements Program Guide is written for the practitioners who manage CDC-funded programs day to day:

• Health department grants managers responsible for application submissions, budget management, financial reporting, and compliance across multiple CDC cooperative agreements
• Epidemiologists and program directors who lead CDC-funded surveillance, prevention, and response activities and are accountable for performance objectives
• Tribal health administrators navigating CDC funding alongside ISDEAA contracts, IHS funding, and other federal streams
• Evaluation and quality improvement staff designing evaluation plans and performance measurement systems for CDC-funded programs
• Fiscal and contracts officers managing sub-awards, procurements, and financial compliance under 2 CFR 200 and 45 CFR Part 75

What This Guide Covers

Each section of this guide addresses a specific aspect of CDC cooperative agreement management. Whether you are preparing your first competitive application or managing a portfolio of CDC awards in Year 4 of the project period, these pages provide the detailed reference information you need.