In June 2009, the World Health Organization officially declared an influenza pandemic. In the United States, the federal government supplied 2009 H1N1 vaccine at no cost and provided funding for states to implement vaccination programs. Vaccine providers including health departments were permitted to bill insurance plans for administering 2009 H1N1 vaccine.

To determine the extent to which local health departments (LHDs) billed for administering 2009 H1N1 vaccine, specific billing practices of LHDs, and factors associated with LHD billing.

Cross-sectional study using an Internet-based survey, and semistructured interviews.

Nationally representative stratified random sample of 527 LHDs in the United States. Interviews were conducted among a convenience sample of LHDs.

Proportion of LHDs reporting billing for administering 2009 H1N1 vaccine.

A total of 308 health departments (58%) provided responses complete enough for analysis. Most LHDs (82%) had previous experience billing for seasonal influenza vaccination, but only 20% (n = 57) billed for administration of 2009 H1N1 vaccine. Medicare (74%) and Medicaid (80%) were the most commonly billed health care payers; more than half (55%) of LHDs billing for 2009 H1N1 vaccine administration sought reimbursement from one or more private insurance plans. Billing for 2009 H1N1 vaccine administration was more common among LHDs that previously offered seasonal influenza vaccination (P = .003), previously billed for seasonal influenza vaccination (P = .04), and conducted school-located influenza vaccination clinics prior to the 2009–2010 influenza season (P = .002).

Most LHDs elected not to bill for 2009 H1N1 vaccine administration despite prior experience billing for influenza vaccination. It is important to understand barriers to billing and resources needed by LHDs to facilitate billing for vaccination. Developing public health billing capacity will allow LHDs to recoup the costs of providing vaccines to insured persons and may also prepare them to conduct billing activities for other services or during future public health emergencies.