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Little is known about the impact of vaccine shortages on vaccination rates among disadvantaged populations in the United States. We compared factors associated with influenza vaccination rates during a vaccine shortage (2004–2005) and a non-shortage (2003–2004) year among adults in predominantly minority New York City neighborhoods. Thirty-one percent of participants received influenza vaccine during the non-shortage year compared with 18% during the shortage. While fewer people received the influenza vaccine during the shortage, a higher proportion of the vaccinated were in a high-risk group (68% vs. 52%, respectively). People were less likely to have been vaccinated during the shortage if they were Black. This study suggests that vaccination rates were lower during the shortage period among Blacks and those who are not explicitly a focus of national vaccination outreach campaigns. Such groups are less likely to be vaccinated when vaccines are scarce.