Few studies have examined potential factors that contribute to low influenza vaccination rates among minority children. This study aimed to assess the prevalence of early childhood influenza vaccination among young black and Latino children, living in inner-city neighborhoods, and examine the effects of child, caregiver and health system factors. Secondary data analysis was performed using a survey about medical home experiences conducted from May 2007-June 2008. The study sample was limited to children ≥6 months in any influenza season prior to the 2006-2007 influenza season. Bivariate analyses and multivariable logistic regression tested associations between influenza vaccination receipt and socio-demographic and health system characteristics. One-third of children received an influenza vaccination by the end of 2006-2007 season, while only 11% received a vaccination within their first season of eligibility. Black children were more likely than Latino children to have been vaccinated (50% vs. 31%, P<0.01) during their first few eligible seasons. Children whose mothers were older, proficient in English, and frequent users of healthcare were more likely to obtain vaccination. Child attendance at healthcare settings with immunization reminder systems was also positively correlated with influenza vaccination. Our findings suggest that initial vaccination receipt among minority children from inner-city communities might be improved by expanded influenza promotion activities targeting younger mothers or those with limited English proficiency. Strategies to increase the frequency of child's actual contact with the medical home, such as reminder systems, may be useful in improving uptake of influenza vaccination among inner-city, minority children.