The seminal vesicles and the prostate are frequently affected by egg-induced inflammation in Schistosoma haematobium infected men. The objective of this study was to assess the semen quality in men with male genital schistosomiasis (MGS). The examination of the semen samples was performed in men aged 15 to 49 years living an S. haematobium endemic area in Madagascar prior to anti-schistosoma treatment with praziquantel and five months later. Men from the high endemic Sirama sugarcane plantation with positive egg excretion in the urine and circulating anodic antigen (CAA) present in serum (n=85) were compared to men (without egg excretion and no CAA) from the neighbouring low-endemic Mataipako village (n=57). The proportion of men with egg excretion in semen was significantly higher in Sirama than in Mataipako (53% versus 4%), whereas the median ejaculate volume was significantly lower in Sirama (1.8 ml versus 2.4 ml). There was no statistical difference in median spermatocyte counts and in the proportions of men detected with azoospermia. The mean apoptotic rate was 7.8% in a subgroup of 30 men from Sirama. A positive correlation was found between apoptotic rate and seminal eosinophil cationic protein (ECP) level (rho=0.560; P<0.001). At follow up, egg excretion and ECP level in semen declined significantly and were paralleled by a significant reduction in the apoptotic rate. The study suggests that S. haematobium infection is associated with sperm apoptosis and a reduced production of seminal fluid. Egg induced inflammation in the seminal vesicles and the prostate could be underlying mechanism for both observations.