As part of a comprehensive human immunodeficiency virus (HIV) prevention strategy targeting high-risk groups, sexually transmitted infection (STI) clinics are offered to all prisoners in Thyolo district, southern Malawi. Prison inmates are not, however, allowed access to condoms as it is felt that such an intervention might encourage homosexuality which is illegal in Malawi. A study was conducted between January 2000 and December 2001 in order to determine the prevalence, incidence, and patterns of STIs among male inmates of 2 prisons in this rural district. A total of 4229 inmates were entered into the study during a 2-year period. Of these, 178 (4.2%) were diagnosed with an STI. This included 83 (46%) inmates with urethral discharge, 60 (34%) with genital ulcer disease (GUD), and 35 (20%) inmates with epididymo-orchitis. Fifty (28%) STIs were considered incident cases acquired within the prisons (incidence risk 12 cases/1000 inmates/year). GUD was the most common STI in this group comprising 52% of all STI. This study shows that a considerable proportion of STIs among inmates are acquired within prison. In a setting of same-sex inmates, this suggests inter-prisoner same-sex sexual activity. The findings have implications for HIV transmission and might help in developing more rational policies on STI control and condom access within Malawi prisons.