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Danish male military recruits (n = 388) were included in a follow-up study to investigate the prevalence and persistence of asymptomatic Chlamydia trachomatis infections. Urine specimens were collected at enrolment and after approximately six months. C. trachomatis was detected by polymerase chain reaction (Amplicor, Roche). Questionnaires were filled out concerning sexual behaviour and clinical symptoms.The prevalence of asymptomatic C. trachomatis in Danish male military recruits was 4.6% (18 out of 388). From five C. trachomatis-positive men no follow-up sample was obtained. From the remaining 13 C. trachomatis-positive men four (31%) were treated for C. trachomatis between the two visits (outside the study protocol). Of the remaining nine men, one cleared the infection and eight men (89%) had a persistent infection. The number of lifetime sexual partners was associated with the presence of C. trachomatis at enrolment. Although based on small numbers, this follow-up study shows, in contrast to women with asymptomatic C. trachomatis infections, a high percentage of C. trachomatis persistence in asymptomatically infected males.