Background: Although male infertility is highly prevalent in sub-Saharan African countries, minimal studies have been undertaken to identify its determinants, factors and root causes. We undertook this study to determine the association between oxidative stress markers and seminal fluid quality parameters among a cohort of Nigerian men attending an infertility clinic at the University of Benin Teaching Hospital in Southern Nigeria. Methods: This comparative cross sectional study involved 90 men attending the infertility clinic at the University of Benin Teaching Hospital, Benin City. The study consisted of 45 participants with abnormal semen parameters and 45 with normal semen parameters. Oxidative stress markers: superoxide dismutase and malondialdehyde levels in semen were assayed in both normal and abnormal semen group using the Adrenalin inhibition method by Misra and Fridovich for Superoxide dismutase and the Thiobarbituric acid assay by Buege and Aust for Malondialdehyde. Data were analysed using univariate, bivariate, and binary logistic regression to test the association between oxidative stress markers and the risk of abnormality in seminal fluid parameters, and Pearson's correlation to assess the direction of association. Results: The mean levels of superoxidase dismutase were higher in the normal group (1.37 u/g ± 0.34) as compared with the abnormal (0.78u/g ± 0.36, p < 0.001). The mean (SD) malondialdehyde level in the control group was (0.59mol/g ± 0.19) and was significantly lower than in the cases (1.38 ± 0.45mol/g, P < 0.001). There was a positive correlation between superoxide dismutase levels and a negative correlation between malondialdehyde levels and sperm concentration, motility and morphology in both cases and controls. However, after adjusting for cofounders in logistic regression, Superoxide dismutase had a statistically significant effect on motility, while Malondialdehyde had a substantial impact on motility and concentration. Conclusion: We conclude that levels of a marker of oxidative stress (Malondialdehyde) are higher in men with poor semen quality. In contrast, levels of the anti-oxidative stress marker (superoxide dismutase) were higher in men with better semen quality. Superoxide dismutase had a significant impact on sperm motility, while Malondialdehyde affected both sperm motility and concentration. We believe these results would serve as an adjunct when evaluating infertile males.