CDC Partnerships with State and Local Health Departments

The Centers for Disease Control and Prevention does not deliver public health services directly to communities in most circumstances — that work flows through a structured system of partnerships with state, territorial, tribal, and local health departments. This page explains how those partnerships are defined, how funding and authority move through the system, what kinds of programs they support, and where CDC's role ends and state or local jurisdiction begins. Understanding this architecture is essential for grasping how federal public health guidance translates into action on the ground.

Definition and scope

CDC's partnerships with state and local health departments are formalized primarily through two legal instruments: cooperative agreements and grants, both administered under Title 42 of the U.S. Code and governed by the Office of Management and Budget's Uniform Guidance (2 CFR Part 200). A cooperative agreement differs from a standard grant in that CDC maintains substantial involvement in program activities — reviewing work plans, approving key decisions, and providing technical assistance — rather than simply disbursing funds and monitoring compliance. Grants, by contrast, allow recipient agencies greater programmatic independence.

The scope of these partnerships spans virtually every domain described across the broader CDC programs and operations. They cover infectious disease surveillance, chronic disease prevention, environmental health monitoring, emergency preparedness, laboratory capacity, and workforce development. As of the fiscal year 2023 President's Budget, CDC distributed more than $5 billion annually through grants and cooperative agreements to public health partners, with state and local health departments representing the largest category of recipients (CDC Congressional Budget Justification FY2023).

The 50 state health departments, 8 U.S. territories and freely associated states, and more than 2,500 local health departments constitute the primary network through which this funding operates. CDC's grants and cooperative agreements framework provides the legal and procedural scaffolding that governs every financial relationship within this network.

How it works

The partnership mechanism follows a structured sequence:

1. Notice of Funding Opportunity (NOFO): CDC publishes a NOFO through Grants.gov or its own grants portal, specifying program objectives, eligibility, funding ceilings, and performance measures.
2. Application and review: State or local agencies submit applications; CDC program staff and independent reviewers score them against published criteria.
3. Award: CDC's Office of Grants Services issues a Notice of Award, which is the legally binding document establishing the terms, conditions, and budget periods — typically 12 months within a multi-year project period.
4. Implementation: Recipient health departments carry out program activities, with CDC providing technical assistance, training, and in some programs, direct staffing support through mechanisms like the Epidemic Intelligence Service.
5. Reporting and monitoring: Recipients submit performance progress reports at intervals specified in the award; CDC program officers review outputs against established performance indicators.
6. Continuation or close-out: Based on performance and appropriations, awards may be renewed for additional budget periods or formally closed out.

Technical assistance is not optional or incidental — it is a defined component of the cooperative agreement structure. CDC staff, including those detailed through the CDC Epidemic Intelligence Service, may be embedded at state health departments to support surveillance, outbreak investigations, and program implementation directly.

Funding flows from Congressional appropriations to CDC, which then sub-awards to states. States may further sub-award to local health departments, counties, or tribal health programs, subject to CDC approval and federal cost principles. This layered flow means that a single CDC program can have three or four jurisdictional layers between federal authorization and community-level delivery.

Common scenarios

Three program types illustrate how partnerships function across different public health domains:

Epidemiological surveillance networks: The National Notifiable Diseases Surveillance System (NNDSS), administered in partnership with the Council of State and Territorial Epidemiologists (CSTE), requires state health departments to report confirmed cases of designated conditions to CDC. States use CDC-funded infrastructure to collect, validate, and transmit these reports. CDC aggregates and publishes the data through the Morbidity and Mortality Weekly Report and the CDC data and statistics resources portal. The partnership here is operational: states collect and report; CDC synthesizes and responds.

Immunization program delivery: Section 317 of the Public Health Service Act authorizes CDC to fund state and local immunization programs. Under this authority, CDC purchases vaccines through centralized contracts and distributes them to states, which in turn manage local distribution through health departments, federally qualified health centers, and provider networks. The CDC vaccination programs operate entirely through this partnership model — CDC does not administer vaccines directly to the public.

Public health emergency preparedness: The Public Health Emergency Preparedness (PHEP) cooperative agreement, authorized under the Public Health Service Act, funds state and local health departments to build and maintain 15 capabilities defined by CDC's public health emergency response framework. These include biosurveillance, emergency operations coordination, and medical countermeasure dispensing. PHEP awards are five-year cooperative agreements, renewed annually within the project period, with each state's funding level tied to a formula that accounts for population and minimum award floors.

Decision boundaries

Understanding where CDC authority ends and state authority begins is critical for interpreting how partnership programs operate in practice.

CDC's authority: CDC sets program objectives, performance standards, and technical guidance. It controls the release of federal funds, can place special conditions on awards for non-compliant recipients, and may withhold continuation funding. CDC's authority and legal powers are grounded in federal statute, but they do not supersede state public health law within state borders.

State and local authority: States hold police powers under the Tenth Amendment, which means that quarantine orders, disease control mandates, and public health regulations within state borders derive from state law, not CDC directives. CDC guidance — including clinical recommendations published through the CDC guidelines and recommendations system — carries no legal enforcement authority at the state level unless a state legislature or agency formally adopts it.

The contrast in practice: A cooperative agreement recipient that declines to implement a CDC-recommended intervention does not face a federal fine or criminal sanction — CDC's primary remedy is financial, specifically the withholding or recoupment of award funds. This differs substantially from regulatory enforcement relationships, such as those between the Environmental Protection Agency and state environmental agencies operating under delegated federal authority, where non-compliance can trigger direct federal enforcement. The CDC-state partnership model depends on alignment of interests and financial incentives rather than command authority.

This boundary also shapes how CDC disease surveillance systems operate: CDC can request data, standardize reporting formats, and fund infrastructure, but it cannot compel a state health department to adopt a specific electronic health information system or reporting protocol absent a statutory mandate. Achieving national data standardization therefore requires sustained negotiation through bodies like CSTE rather than unilateral federal rulemaking.