During 2001 and 2002 in the United States, there were unprecedented shortages in 5 of the 8 routinely recommended childhood vaccines. These included diphtheria and tetanus toxoids and acellular pertussis (DTaP) vaccine; varicella vaccine; measles-mumps-rubella (MMR) vaccine; and pneumococcal conjugate vaccine. Supplies of adult tetanus and diphtheria toxoids also were affected.1–4 The Advisory Committee on Immunization Practices (ACIP) is the federal advisory committee charged with providing “advice and guidance to the Secretary, the Assistant Secretary for Health, and the Centers for Disease Control and Prevention (CDC) on the most effective means to prevent vaccine-preventable diseases.”5 The shortage of DTaP, which began in January 2001 and ended in July 2002, prompted the ACIP and CDC to issue the interim recommendation that health care providers with inadequate DTaP supplies defer the fourth dose of the vaccine (DTaP4).1,2 The CDC also worked to ensure the equitable distribution of available public sector vaccine through rigorous tracking of state inventories, establishing state allocation amounts, and prioritizing vaccine shipments.6 The intent was to ensure an adequate supply of vaccine for the vaccination of infants with the first 3 doses of DTaP vaccine. These efforts, along with consistent adherence by providers to interim guidelines to defer the fourth dose, should have resulted in ample supplies of the first 3 doses and an associated uniform decline in DTaP4 coverage for all children in the United States. Despite the CDC’s efforts, public sector DTaP vaccine supply was more severely affected by the DTaP shortage than was private sector vaccine supply.7 In addition, previous studies have shown that timely and equitable administration of vaccines during national shortages can be problematic.6–8 A survey of providers and state immunization programs found that only 16% of the providers implemented the interim ACIP recommendations to suspend the DTaP4.6 A second study assessed the effect of the vaccine shortage on coverage with data from the National Immunization Survey. This study found that children who received vaccines at public clinics and children residing in certain geographic regions experienced significantly greater declines in DTaP4 coverage than did children served by private providers or in other regions of the United States. The investigators concluded that these children were differentially affected by the shortage and that such inequities of effect should be corrected.8 The Indian Health Service (IHS) is the federal health care provider for eligible American Indian/Alaska Native (AIAN) people in the United States, with a network of hospitals and clinics serving AIAN people in 35 states. The IHS provides clinical services to 1.6 million of the 2.5 million US AIAN population.9 The IHS is divided into 12 administrative regions called “Areas.” Immunization coverage for children served by IHS, Tribal, and Urban Indian health facilities is monitored on a quarterly basis. Each of the 12 IHS Areas submits an aggregate report on all children aged 3 to 27 months who have ever been seen at an IHS, Tribal, or Urban Indian health facility and reside in a community located in the catchment area of the facility. These reports monitor age-appropriate vaccine coverage with DTaP, inactivated poliovirus (IPV) vaccine, MMR vaccine, Haemophilus influenzae type b (Hib) vaccine, hepatitis B vaccine, pneumococcal conjugate vaccine, varicella vaccine, and hepatitis A vaccine. The IHS quarterly reporting system differs from the National Immunization Survey in 2 important ways: (1) it includes children younger than 19 months; and (2) it is not sample based—rather, it is designed to capture the entire population of AIAN children seen at participating facilities. The coverage reported by the 12 IHS Areas thus can be combined to provide an overall picture of coverage for IHS. In September 2002, the IHS implemented more stringent reporting guidelines aimed at achieving more inclusive and more accurate reporting of childhood immunization coverage. As a result of these changes, the IHS quarterly reports now capture approximately 60% of the total 3- to 27-month-old IHS user population, compared with 40% or less in previous years (IHS, unpublished data, 2004). All AIAN children are eligible to receive public sector vaccine through the federally funded Vaccines for Children program. Under this program, vaccine is ordered and distributed by the state to public and private clinics for eligible patients at no cost to the facility. AIAN children can receive Vaccines for Children (VFC) vaccines at IHS and tribal clinics as well as at other public and private providers that are part of the VFC program. Because all IHS, Tribal, and Urban Indian health facilities receive VFC vaccines, data from the IHS immunization coverage reports on children who receive immunizations from these sites provide insight into the effect the DTaP shortage had on DTaP4 coverage for a small group (< 3% of all VFC vaccine) of children receiving VFC vaccines. This study analyzed changes in IHS immunization coverage; determined the effect of the DTaP shortage on DTaP4 coverage among AIAN children; and explored possible inequities in vaccine supply, distribution, and coverage during the national shortage.