Approximately 600 bp of ATP synthase subunit 6 mitochondrial gene (ATP6) were amplified and sequenced for 110 semen samples collected from infertile and normal Saudi men inhabiting Riyadh province. These data were analyzed in order to identify the Single Nucleotide Polymorphisms (SNPs) associated with male infertility. Six silent substitutions G8697A, G8856A, T8889C, T8952C, C9075T and C9060A were recorded with one novel site (G8856A) in the infertile men. Seven non-synonymous substitutions were also obtained with 4 novel sites (C8684T, G8860A, C8876T and G9055A) in the infertile men. Nine haplogroups (H2a, H1a, H5a, T, J2a, K1a, N1b, M25 and U7) were predicted. H5a, M25 and U7 were found in the oligoasthenoteratospermic (AOT) infertile men only with a percentage of 4.5%. It could be concluded that there was a correlation between ATP6 substitutions/haplogroups and male infertility since specific SNPs and haplogroups appeared in the AOT infertile men only. The present results are considered preliminary for using the mitogenome of the infertile men in a forensic perspective. More mtDNA data from infertile men are necessary to assess mtDNA forensic contributions in male fertility. Examination of autosomal Short Tandem Repeats (STRs) and Y chromosome-STR profiles for infertile men should be conducted to ascertain any changes in the genetic loci.