Little is known about whether disparities occur within or between hospitals for national Hospital Quality Alliance (HQA) measures. We examined patient-level data from 4,450 non-federal hospitals in the US for over 2.3 million Black, Hispanic, Asian, American Indian/Alaska Native, and Native Hawaiian/Pacific Islander patients who received care for acute myocardial infarction, heart failure, or pneumonia in 2005. There were 37 out of 95 findings of disparities after adjusting for patient characteristics. Eleven of the disparities were explained entirely by where minorities received care and the magnitude for 25 of the others was substantially reduced after adjusting for site of care. Adjusting for between-hospital quality differences accounted for a large proportion of the disparities. Where disparities exist, the primary cause may be that minorities are more likely to receive care in lower-performing hospitals. Policies to reduce disparities should include targeting resources to facilities serving a high percentage of minority patients.