CDC Cooperative Agreement Eligibility

Understanding CDC Eligibility

Unlike formula-based programs such as CSBG where eligibility comes through state designation, CDC cooperative agreement eligibility is determined by each individual NOFO. Every Notice of Funding Opportunity published by CDC specifies exactly which types of organizations may apply, and these eligibility requirements vary significantly across CDC centers, divisions, and program areas. There is no single set of CDC eligibility criteria that applies universally.

This means that the first step in assessing eligibility for any CDC cooperative agreement is reading the NOFO carefully — specifically the "Eligible Applicants" section, which typically appears in Section C of the NOFO. Assumptions based on eligibility for one CDC program do not necessarily apply to another.

Eligible Applicant Types

While eligibility varies by NOFO, CDC cooperative agreements generally target the following categories of applicants. Each NOFO will specify which of these types are eligible for that particular opportunity.

State Health Agencies

State health departments and state health agencies are the primary recipients of most CDC cooperative agreements. Programs like PHEP (CFDA 93.069), ELC (CFDA 93.323), immunization (CFDA 93.268), and chronic disease prevention (CFDA 93.735) typically award directly to the official state health agency. In some states, this is a standalone department of health; in others, public health functions are housed within a larger human services or health and human services agency.

For many CDC programs, the state health agency is the only eligible applicant type, and the agency is expected to sub-award to local health departments, universities, and community-based organizations as needed to accomplish program objectives. This creates a pass-through structure where the state is both a recipient and a funder.

Local Health Departments

Large local health departments — particularly those in major metropolitan areas with populations over 500,000 — are often eligible to apply directly for CDC cooperative agreements. Many CDC programs include "directly funded" categories for large cities and counties whose public health infrastructure justifies a direct federal relationship. Examples include directly funded HIV prevention programs in high-burden jurisdictions and PHEP awards to major metropolitan health departments.

Smaller local health departments typically access CDC funding through sub-awards from their state health agency rather than through direct applications. The NOFO will specify whether local health departments may apply directly or must participate through the state.

Tribal Organizations and Tribal Health

Federally recognized tribes, tribal organizations (as defined under the Indian Self-Determination and Education Assistance Act), and tribal epidemiology centers are eligible for many CDC cooperative agreements. CDC engagement with tribal communities occurs through multiple pathways:

• Direct tribal applicants: Many NOFOs include tribes and tribal organizations as eligible applicant types. Some programs create separate funding categories or set-asides for tribal applicants with dedicated review panels and adjusted scoring criteria.
• Tribal epidemiology centers (TECs): The 12 tribal epidemiology centers serve as public health authorities for their regions and are eligible for CDC surveillance and epidemiology cooperative agreements. TECs play a critical role in tribal disease surveillance and data sovereignty.
• ISDEAA pathways: For certain programs, tribal organizations may access CDC-related public health functions through Indian Self-Determination Act compacting or contracting, particularly for programs historically administered by the Indian Health Service (IHS).
• CDC Office of Tribal Affairs and Strategic Alliances (OTASA): OTASA coordinates tribal engagement across CDC and can help tribal organizations navigate the landscape of available CDC funding.

Tribal applicants should note that CDC cooperative agreement award sizes for tribal organizations often range from $100,000 to $500,000 annually — smaller than state-level awards but significant for tribal health infrastructure. Some programs provide tiered funding based on the size of the population served.

Universities and Research Institutions

Academic institutions are eligible for many CDC cooperative agreements, particularly those focused on research, evaluation, training, and technical assistance. CDC funds numerous university-based centers of excellence, prevention research centers, and academic health department partnerships. Universities applying for CDC cooperative agreements must demonstrate both the scientific capacity and the practice-oriented partnerships needed to translate research into public health action.

Nonprofit Organizations

501(c)(3) nonprofits are eligible for selected CDC cooperative agreements, particularly those focused on community-based health promotion, disease prevention education, and population-specific interventions. Community-based organizations (CBOs) play a significant role in CDC HIV prevention, chronic disease prevention, and environmental health programs. Nonprofits must demonstrate organizational capacity, relevant experience, and the infrastructure needed to manage federal funds in compliance with 2 CFR 200 and 45 CFR Part 75.

Territorial Health Agencies

U.S. territories (Puerto Rico, U.S. Virgin Islands, Guam, American Samoa, Commonwealth of the Northern Mariana Islands, Republic of the Marshall Islands, Republic of Palau, and the Federated States of Micronesia) are eligible for most CDC cooperative agreements alongside states. Territorial health agencies often receive minimum allocation amounts under formula-based programs like PHEP and immunization cooperative agreements.

Registration Requirements

All applicants for CDC cooperative agreements must complete several federal registrations before they can submit an application. These registrations take time — often 4 to 8 weeks for initial setup — so organizations planning to apply for a CDC NOFO should ensure their registrations are current well before the application deadline.

SAM.gov Registration and UEI

Active registration in the System for Award Management ( SAM.gov) is a prerequisite for any federal award, including CDC cooperative agreements. SAM.gov registration assigns your organization a Unique Entity Identifier (UEI), which replaced the legacy DUNS number in April 2022. Key requirements include:

• Active registration status: Your SAM.gov registration must be active (not expired) at the time of application submission and must remain active throughout the award period
• Annual renewal: SAM.gov registrations expire annually. Set a calendar reminder to renew at least 30 days before expiration to avoid lapses that can delay award processing
• Entity validation: SAM.gov performs entity validation using IRS and state business records. Discrepancies between your SAM.gov registration and other federal records can cause delays

Grants.gov Registration

All competitive CDC cooperative agreement applications are submitted through Grants.gov. Your organization must register on Grants.gov and designate an Authorized Organization Representative (AOR) who is authorized to submit applications on behalf of the organization. The AOR registration process includes an e-Business Point of Contact (EBiz POC) authorization step that must be completed before the AOR can submit.

First-time Grants.gov registration can take 2 to 4 weeks. Organizations that already have active registrations should verify their AOR credentials and submission capabilities at least 2 weeks before any application deadline.

eRA Commons (for Some Programs)

Some CDC cooperative agreements, particularly those involving research components, require registration in the NIH eRA Commons system. The NOFO will specify whether eRA Commons registration is required. If so, both the organization and the principal investigator/project director must have active eRA Commons accounts.

State vs. Local Applicant Considerations

Many CDC programs create a two-tier structure: state health agencies are direct recipients, and local health departments access funding through sub-awards from the state. This structure has significant implications for both eligibility and compliance:

• Direct recipients (states): Bear full responsibility for compliance with 45 CFR Part 75, CDC terms and conditions, and program-specific requirements. Also responsible for monitoring sub-recipients.
• Sub-recipients (locals): Must comply with applicable federal requirements as flowed down through the sub-award agreement. Subject to monitoring by the state pass-through entity. Must provide data and reports to the state on schedule.
• Directly funded locals: Large jurisdictions that receive CDC funding directly bear the same compliance responsibilities as state agencies and must maintain their own financial management infrastructure, reporting systems, and audit capacity.

Consortium and Coalition Approaches

Some CDC NOFOs encourage or require consortium or coalition-based applications. In these cases, a lead applicant submits on behalf of a group of organizations that will collectively carry out the scope of work. Common consortium structures include:

• Multi-jurisdictional partnerships: Multiple local health departments applying together through a lead agency to address cross-jurisdictional public health challenges
• Academic-practice partnerships: A university and a health department applying jointly, with the university contributing evaluation and research capacity and the health department providing practice infrastructure
• CBO coalitions: A lead nonprofit organization applying on behalf of a coalition of community-based organizations serving specific populations (e.g., HIV prevention CBOs in a metropolitan area)

When applying as a consortium, the lead applicant is the legal recipient of the award and bears full compliance responsibility. Consortium members receive sub-awards and are subject to sub-recipient monitoring requirements under 45 CFR Part 75.

Sub-Recipient vs. Contractor Distinction

One of the most important — and frequently misunderstood — eligibility and compliance concepts is the distinction between sub-recipients and contractors. Under 2 CFR 200.331 (implemented by 45 CFR 75.351 for HHS awards), this distinction determines which compliance requirements apply to each downstream entity.

Getting this classification wrong has real consequences. If an entity that should be classified as a sub-recipient is treated as a contractor, it may escape the monitoring and compliance requirements that apply to federal sub-awards. If a contractor is misclassified as a sub-recipient, you may impose unnecessary compliance burdens and audit requirements. Review the substance of each relationship, not just the label, when making this determination.

Eligibility Checklist

Use this checklist to verify your organization's readiness to apply for a CDC cooperative agreement:

• Confirmed that your organization type is listed as eligible in the target NOFO
• Active SAM.gov registration with current UEI (not expired or pending renewal)
• Grants.gov registration complete with designated AOR and EBiz POC authorization
• eRA Commons registration (if required by NOFO) with PI/PD account active
• No active exclusions or debarments listed on SAM.gov
• Current Single Audit filed (if organization expends $750,000+ in federal awards annually)
• Negotiated indirect cost rate agreement current (or plan to use 10% de minimis rate)
• Financial management system capable of tracking federal funds by award and cost category
• Organizational capacity to comply with CDC reporting timelines and data system requirements
• Key personnel identified with qualifications matching NOFO requirements