Despite growing inmate populations in the USA, inmates are excluded from most national health surveys and little is known about whether the prevalence of chronic disease differs between inmates and the non-institutionalised population. Nationally representative, cross-sectional data from the 2002 Survey of Inmates in Local Jails, 2004 Survey of Inmates in State and Federal Correctional Facilities and 2002-4 National Health Interview Survey Sample Adult Files on individuals aged 18-65 were used. Binary and multinomial logistic regression were used to compare the prevalence of self-reported chronic medical conditions among jail (n = 6582) and prison (n = 14,373) inmates and non-institutionalised (n = 76 597) adults after adjusting for age, sex, race, education, employment, the USA as birthplace, marital status and alcohol consumption. Prevalence and adjusted ORs with 95% CIs were calculated for nine important chronic conditions. Compared with the general population, jail and prison inmates had higher odds of hypertension (OR(jail) 1.19; 95% CI 1.08 to 1.31; OR(prison) 1.17; 95% CI 1.09 to 1.27), asthma (OR(jail) 1.41; 95% CI 1.28 to 1.56; OR(prison) 1.34; 95% CI 1.22 to 1.46), arthritis (OR(jail) 1.65; 95% CI 1.47 to 1.84; OR(prison) 1.66; 95% CI 1.54 to 1.80), cervical cancer (OR(jail) 4.16; 95% CI 3.13 to 5.53; OR(prison) 4.82; 95% CI 3.74 to 6.22), and hepatitis (OR(jail) 2.57; 95% CI 2.20 to 3.00; OR(prison) 4.23; 95% CI 3.71 to 4.82), but no increased odds of diabetes, angina or myocardial infarction, and lower odds of obesity. Jail and prison inmates had a higher burden of most chronic medical conditions than the general population even with adjustment for important sociodemographic differences and alcohol consumption.