The presence of DNA fragmentation in semen is associated with poor results in ART (Assisted Re-productive Technology). This has led to the introduction of sperm DNA integrity testing in the clinical assessment of male infertility. The TUNEL assay is one of the most commonly used tests to measure DNA fragmentation in research studies, but it is now being optimized for routine clinical use. So, the objectives of our study were to install the TUNEL assay in our laboratory and to use it to assess the degree of DNA fragmentation in our patients dealing with couple infertility. Forty seven (47) and 25 samples from patients followed up for infertility and known fertile men were analyzed between August 2013 and July 2015 respectively. The sperm samples were evaluated according to the World Health Organization Guidelines. Sperm DNA damage was assessed by the TUNEL assay, with a standardized protocol that we adapted for reading using fluorescence microscopy instead of flow cytometry. The Sperm DNA Fragmentation Index was significantly higher in patients with infertility compared to the controls (22.2% ± 5.6% vs. 16.7% ± 0.7%) with a p < 0.05. This Index was also high in patients with varicocele compared to the control group (22.8% ± 9.2 vs. 16.7% ± 0.7%) (p < 0.01). After establishing the ROC curve (Receiver Operating Characteristics curve), we found a 15% threshold of DNA fragmentation, separating the patients with infertility from the control group. In our study, a 15% threshold positivity of DNA fragmentation using the TUNEL assay was highly associated with infertility. The results indicate that high level DNA fragmentation is associated with infertility.