Background The impact of vaccine shortages on disparities in influenza vaccination is uncertain. Purpose The objective of this research was to examine the association between influenza vaccine supply and racial/ethnic disparities in vaccination rates among elderly Medicare beneficiaries. Methods Cross-sectional multivariable logistic regression analyses were performed in 2010 to examine whether racial/ethnic disparities in vaccination rates changed across two consecutive seasons: from (Period 1) 2000–2001 and 2001–2002 seasons through (Period 4) 2003–2004 and 2004–2005 seasons. Self-reported receipt of influenza vaccine across consecutive years was examined among community-dwelling non-Hispanic African-American (AA); non-Hispanic white (W); English-speaking Hispanic (EH); and Spanish-speaking Hispanic (SH) elderly enrolled in the Medicare Current Beneficiary Survey (unweighted n=2306–2504, weighted n=8.23–8.99 million for Periods 1 through 4). Results During Periods 1 and 2, when vaccine supply increased nationally, adjusted racial/ethnic disparities in the influenza vaccination rate decreased by 1.8%–7.4% (W–AA disparity); 4.5%–6.6% (W–EH disparity); and 6.6%–11% (W–SH disparity) (all p<0.001). During Period 4, when vaccine supply declined, adjusted disparities in vaccination rates increased by 2.3% (W–AA disparity) and 6.1% (W–EH disparity) but decreased by 6.6% (W–SH disparity) probably due to a “floor effect” (constant low rates among SH; all p<0.001). Conclusions Improved vaccine supply was generally associated with reduced racial/ethnic disparities in influenza vaccination rates, whereas worse supply was associated with increased disparities. To avoid future widening of racial health disparities, policy options include stabilizing the vaccine supply and preferential delivery of vaccines to safety-net providers serving AA and Hispanic populations during a shortage.