The singular focus on self-identified race and ethnicity in health disparities research may not fully convey the individual and structural components of experiencing race in society, or in a racialized context such as prison. Processes of racialization create boundaries between incarcerated individuals and regulate their daily interactions and access to resources, with possible effects on well-being. However, the relationship between perceived race and health has not been examined within the imprisoned population. We used data from the 2016 Survey of Prison Inmates (n = 23,010) to assess how self-identified race, perceived race, and the discordance between racial self-identification and perception were associated with the physical (number of chronic conditions) and mental health (psychological distress) of American Indian and Alaska Native, Asian, Black, Latino, White, and multiracial incarcerated individuals. Reported perception as Latino was associated with better mental and physical health relative to perception as White. Perceived Latino identity was more strongly associated with physical and mental health than a Latino self-identity. Reported perception as Black was associated with less psychological distress than perception as White, but this relationship dissipated after accounting for self-identified race. In contrast, perceived and self-identified multiracial incarcerated individuals reported worse health than their White counterparts. Having a discordant (vs. concordant) racial identity was associated with worse physical and mental health among imprisoned persons regardless of race. The use of a single, unidimensional measure of race and ethnicity in health disparities research does not fully reveal racialization's influence on health, specifically for those experiencing incarceration.