Background : Transgender individuals are known to be at a higher risk for certain chronic conditions compared to cisgender individuals. Similarly, research also shows justice-involved individuals have a higher risk of chronic conditions compared to non-justice-involved individuals. Aim : This study aims to investigate the differences in chronic disease diagnoses between transgender and cisgender individuals who either utilized healthcare services provided by a US county health system or who were incarcerated in the same county's jail. Method : We leveraged electronic health record data from a United States county health system, including data from the local jail, to evaluate the difference in diagnosis of certain chronic conditions among transgender and cisgender individuals. We also compared individuals who experienced incarceration and those who did not. Results : We found transgender individuals experiencing recent incarceration were more likely to be diagnosed with substance use disorder, HIV/AIDS, and Hepatitis C than cisgender individuals. Transgender individuals not experiencing recent incarceration were more likely to be diagnosed with HIV/AIDS, seizure disorder, major depressive disorder, and bipolar disorder than cisgender individuals. Conclusion : These results highlight how transgender individuals may be disproportionately impacted by certain diseases within and outside carceral settings.