First catch early morning urine samples were compared to urethral swabs for detection of Chlamydia trachomatis in 405 male military conscripts, using 2 enzyme immunoassays, Syva Microtrak EIA (SME) and ABBOT Chlamydiazyme (AC). The prevalence rate of C. trachomatis was 7.9% (95% confidence limits 5.5%-11.0%), and the asymptomatic carrier rate was 7.8% (95% confidence limits 5.2%-11.2%). Only 5 of 32 conscripts with positive test results for C. trachomatis complained of urethritis symptoms, and of 13 conscripts with symptoms, only 5 had positive test results for C. trachomatis. The sensitivity of SME in detecting C. trachomatis was 82.1% for both urine samples and urethral swabs. Assayed with AC, the sensitivity was 62.1% for urine samples and 41.4% for urethral swabs (P > 0.05). With urine as specimen type, the sensitivity of SME was 82.8% and the sensitivity of AC was 62.1% (P > 0.05). With urethral swab as specimen type, the sensitivity of SM E was 92.3% and the sensitivity of AC was 46.1% (P < 0.01). In all assays, the specificity was at least 98.0%. First catch early morning urine seems to be a valid specimen type for the detection of C. trachomatis in young men in comparison to ordinary urethral swab specimens. It is a noninvasive method and suitable for screening of asymptomatic young men.