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Background. A national shortage of heptavalent pneumococcal conjugate vaccine (PCV7) occurred from September 2001 through May 2003. In December 2001 and January 2002, the Advisory Committee on Immunization Practices and the American Academy of Pediatrics (AAP) issued PCV7-shortage recommendations, emphasizing that all health care providers decrease the number of doses for healthy children so that more children could receive some PCV7. Objectives. We assessed (1) how the PCV7 shortage affected pediatricians, (2) whether children in the public and private sectors were vaccinated differently during the shortage, (3) pediatricians' knowledge of and adherence to the Advisory Committee on Immunization Practices/AAP recommendations, (4) and what factors were associated with nonadherence to the recommendations. Methods. We conducted a cross-sectional mail survey of 2500 US physician-members of the AAP from November 2002 through March 2003; physicians providing childhood immunizations were eligible. We asked about PCV7-shortage experience, assessed recommendation adherence through clinical scenarios, and modeled potential factors associated with reported nonadherence to the recommendation to defer the fourth PCV7 dose. Results. Of 2478 surveys sent to valid addresses, 1412 (57%) completed surveys were received; 946 (67%) of these were from eligible pediatricians. Overall, 79% experienced a PCV7 shortage, 94% reported being aware of the recommendations, and 42% reported barriers to recommendation adherence. Ninety-four percent reported vaccinating 6-month-old infants with private or public insurance in the same manner. As recommended, 91% reported fully vaccinating high-risk patients. Contrary to recommendations, 49% reported sometimes or always administering the fourth PCV7 dose to healthy children 12 to 15 months old; their reasons included recurrent otitis media, childcare attendance, and parental desire. Controlling for other characteristics, pediatricians who had no PCV7 shortage in their practices were significantly more likely to report administering the fourth dose than pediatricians who had a shortage (odds ratio [OR]: 3.67; 95% confidence interval [CI]: 2.40–5.63). Other factors associated with nonadherence were being in solo private practice (OR: 2.18; 95% CI: 1.26–3.77) or being male (OR: 1.51; 95% CI: 1.08–2.12). Among pediatricians deferring PCV7, 36% reported having no system to track children for whom PCV7 was deferred. Conclusions. Many pediatricians, both with and without a PCV7 shortage, administered more PCV7 doses than recommended. Pediatricians without a shortage were less likely to limit use, which suggests that they might have focused on the perceived value of administering the full schedule to their patients in preference to broader public health goals. Providing more information to physicians on the effectiveness of a fewer-dose schedule and the risk of disease when vaccine is deferred and educating parents might increase adherence to recommendations and achieve more equitable coverage during vaccine shortages.