Much is known about the role of Chlamydia trachomatis in female infertility, although the same cannot be said about the organism's role in male infertility. Recently, a number of workers have provided a possible explanation of the pathogenesis of C. trachomatis in male infertility and have suggested further studies. Unfortunately, current screening recommendations for C. trachomatis in an infertile couple are vague and unhelpful and many do not even mention this type of screening in the male. To enable any progress to be made in this field, it is essential that investigators know how best to detect C. trachomatis, especially in the male. It is important therefore, to know which specimen is best for C. trachomatis detection with respective strengths and weaknesses of each specimen. Similarly, it is equally important to have a knowledge of which test is appropriate for the type of specimen being examined. It is concluded that for the routine detection of C. trachomatis in males, first void urine is currently the specimen of choice. Moreover, the best detection protocols in the developed world are based on molecular diagnosis of first void urine. These methods provide the best combination of sensitivity and specificity which are currently available on a clinical sample that can be self-taken. Interestingly, as semen is routinely collected for analysis in males of infertile couples, it is suggested that protocols are developed for the optimal detection of C. trachomatis in this specimen, as semen might provide additional information on infection of the upper genital tract, which may not be detected in first-void urine. Finally, the importance of comparing tests for C. trachomatis detection in updating our knowledge has been highlighted by the inability of some molecular methods to detect the new variant strain of C. trachomatis.