Although Chlamydia trachomatis causes symptomatic infection in the lower genital tract of approximately 50% of men, its role in the upper genital tract is less well known. Moreover, for a number of reasons, mostly based on methodological aspects, the impact of chlamydia on semen quality is controversial. Overall, in-vivo studies of C trachomatis in men have provided conflicting evidence as to whether it is associated with reduced fertility. By contrast, in-vitro studies show that co-incubation of spermatozoa with chlamydia causes a significant decline in numbers of motile sperm and results in premature sperm death. Since evidence suggests that chlamydial lipopolysaccharide is the principal factor leading to sperm apoptosis, a new line of inquiry would be to measure the levels of lipopolysaccharide in semen and relate these to parameters of semen quality, including that of sperm function. If these new lines of inquiry are proven, this could lead to potentially novel approaches in the treatment of infertile men.