International studies have consistently shown that the prevalence of poor mental health among prisoners is considerably higher than in the community. To date, however, little is known about the prevalence of psychiatric morbidity in Belgian prisons. In order to fill this gap, the present study reports findings from a sample of 1326 prisoners (1203 men and 123 women), randomly selected from 15 Flemish prisons. An estimated 46.3% of all prisoners were formally diagnosed with a psychiatric disorder at some point during their lifetime, and 40.4% report a history of psychiatric treatment before their incarceration. Severe psychological distress during the past month while incarcerated, as quantified by a GHQ-score ≥7, was identified in more than one-third of the sample (37.3%). Frequent use of mental health services within prison was reported by one in ten respondents (10.8%). The results consistently indicate significantly higher prevalence rates among female prisoners, compared to their male counterparts. Overall, the current study highlights the importance of mental health care being available for inmates in Flanders. Evidence-based interventions are likely to reduce psychological distress, recidivism and subsequent return to prison.