The aim of the study were to estimate the frequency of Y chromosome microdeletion in infertile men from a new geographical ethnic region, Chennai, South East India, to explore the effect of smoking, alcohol drinking, chemical exposure and cellular chromosomal aberration on the frequency of infertility in 34 azoospermia and 55 oligospermia patients. The frequency of Y chromosome microdeletion was estimated using 12 STS markers and the chromosomal aberrations were estimated in leukocyte cultures. In azoospermia the frequency of microdeletions in AZFa, AZFb, AZFc and AZFd were 27, 4, 56 and 13% respectively. In oligospermia they were 33, 7, 48 and 12% in the same order. These frequencies of Y chromosome microdeletion are significantly higher than that of European population. The chromosome aberrations per cell in azoospermia and oligospermia were higher than that of the control at the level of p > 0.001. The percentage of microdeletion observed in unexposed azoospermia had 15%, azoospermia smokers 22%, azoospermia smokers and alcoholics 25%; whereas the unexposed oligospermia had 7%, oligospermia smokers 12%, oligospermia smokers and alcoholics 37%. It seems that the etiology of male infertility may differ between ethnic populations and smoking, alcohol drinking and chemical exposure may have deleterious effect on human fertility.