The aim of this study was to evaluate the influence of different periods of abstinence on conventional semen parameters as well as functional parameters in human semen, including mitochondrial function, chromatin packing and sperm DNA fragmentation. We recruited a cohort of 2,458 men undergoing infertility investigation. Semen analyses were performed according to WHO guidelines/morphology-motile sperm organelle morphology examination/MSOME. For DNA integrity analysis, the percentages of DNA fragmentation (TUNEL), abnormal chromatin packaging/underprotamination (chromomycin A3/CMA3), abnormal mitochondrial membrane potential (MMP/MitoTracker Green), and apoptosis (annexin-V) were recorded. Associations between the sexual abstinence period and sperm parameters were assessed using Spearman correlation. For group comparisons, the subjects were categorized according to the sexual abstinence period (SAP) into three groups: SAP <2 days, SAP 2-5 days, and SAP >5 days. The duration of abstinence had a statistically significant positive influence on sperm concentration and volume, the number of leukocytes and a statistically significant negative influence on sperm motility and vitality. The percentages of DNA fragmentation and MMP (mitochondrial damage) worsened with the increased duration of abstinence. The percentage of sperm protamination was statistically significantly increased with abstinence. Increase in the sexual abstinence period influences sperm quality. This study reinforces the importance of the duration of ejaculatory abstinence on semen parameter variation. It highlights the deleterious effect of increased abstinence on DNA damage, which is most likely associated with ROS (mitochondrial damage/number of leukocytes). The increase in chromatin packaging can represent a protective feature for DNA.