Male infertility, inability to fecundate the oocyte, is due to alterations of sperm characteristics (low number, low motility, altered morphology), to the quantity of semen or to the presence of alterations in the male genital line. 75% of infertile men deal with untreatable sub-fertility. Semen of 200 idiopathic astenozoospermic patients and individuals with normal seminal parameters as control, were analyzed. Results showed that mtDNA and Y chromosome regions from the motile fractions of patients and controls gave amplifications, while, the non-motile fractions of the same seminal samples did not give amplifications of ND5, ND6 and regions inside the D-loop (Carra E. et al.2002, 2004). We recently submitted the DNA of the same patients to 50 different PCR assays using primers covering 25 mtDNA loci to amplification of short and long DNA regions. The results show that only for 14 patients exhibited the predicted PCR products. For the remaining 36 patients we found deletions in the genes coding for the subunits COI, COII, ND5 and ND6 and for the cytochrome b (CYTb). We then related the deletions to sperm motility percentage, in order to contribute to a more precise and complete diagnosis of male infertility.