Toxoplasmosis is the most common, widespread disease in the world which is caused by Toxoplasma gondii.The objective of the current study is to determine the effect of the Toxoplasma gondii infection on male sperm, especially on the mitochondria of sperm for men who suffer infertility and the possibility of a hereditary mutation. Sixty seminal fluid and serum samples were taken from sub- fertile patients who attended Teba center for in vitro fertilization / Babylon and similarly samples were also obtained from healthy individuals as a control group, their ages ranged from 20 to 60 years old during the period from 1st may /2016 till 25th January/2017. All samples subjected to the tests included Macroscopic and microscopic examination, molecular methods was used for DNA extraction, amplification and sequencing. Statistical analysis showed non-significant differences (P<0.01) among age groups and ) between rural 41(68%) and urban 19(32%). However, sperm motility and count recorded highly significant differences (P<0.01) in the mean value for healthy (74.85, 68.017) as compared with the patients (10.30, 10.217). There were also a significant differences (P<0.01) in the mean concentration of Ant-Toxoplasma IgG antibody (1.327μ/ml) in comparison with control group (0.564μ/ml). A highly significant differences (P<0.01) was detected when comparing the positive 55(92%) and negative 5(8%) samples for oligospermia and a significant difference (P<0.05) for Asthenospermia 21(35%), 39(65%). Two mutation 2(3%) were detected in the exchange for fifty eight 58(97%) with a highly significant difference (P<0.01). It was found that the mutation occurred in Asthenospermia of ND1 gene in the site SNP T4216C (T to C) and the site SNP C3450T (C to T) of Mitochondrial DNA. This study confirmed that a mutation in the ND1 gene that is located in the mitochondria of sperms, specifically in people who suffer from infertility, is occurred due to Toxoplasma gondii.