Previously published analyses showed that inequalities in mortality rates between residents of poor and wealthy neighborhoods in New York City (NYC) narrowed between 1990 and 2000, but these trends may have been influenced by population in-migration and gentrification. The NYC public housing population has been less subject to these population shifts than those in other NYC neighborhoods. We compared changes in mortality rates (MRs) from 1989-1991 to 1999-2001 among residents of NYC census blocks consisting entirely of public housing residences with residents of nonpublic housing low-income and higher-income blocks. Public housing and nonpublic housing low-income blocks were those in census block groups with > or =50% of residents living at <1.5 times the federal poverty level (FPL); nonpublic housing higher-income blocks were those in census block groups with <50% of residents living at <1.5 times the FPL. Information on deaths was obtained from NYC's vital registry, and US Census data were used for denominators. Age-standardized all-cause MRs in public housing, low-income, and higher-income residents decreased between the decades by 16%, 28%, and 22%, respectively. While mortality rate ratios between low-income and higher-income residents narrowed by 8%, the relative disparity between public housing and low-income residents widened by 21%. Diseases amenable to prevention including malignancies, diabetes, and chronic lung disease contributed to the increased overall mortality disparity between public housing and lower-income residents. These findings temper previous findings that inequalities in the health of poor and wealthier NYC neighborhood residents have narrowed. NYC public housing residents should be a high-priority population for efforts to reduce health disparities.