Abstract Study question To investigate the association of high DNA stainability (HDS) with fertilization, embryonic development and clinical outcome after IVF treatment. Summary answer Increased HDS levels might be associated with decreased fertilization of IVF cycle. What is known already The HDS parameter of sperm suggests loosening and weakening of chromatin condensation structure resulting from the lack of full histone-to-protamine exchange. Elevated HDS may negatively correlate with sperm quality, including sperm morphology and concentration. Study design, size, duration Couples that underwent IVF cycles from January 2016 to December 2020 were retrospectively studied, including a total of 2604 target cycles after IVF treatment consisting of 676 cycles in the HDS > 15% group and 1928 cycles in the HDS ≤ 15% group. In addition, 548 cycles undergoing fresh IVF-embryo transplantation treatment consisting of 151 cycles in the HDS > 15% group and 397 in the HDS ≤ 15% group were included. Participants/materials, setting, methods HDS was assessed by sperm chromatin structure assay method. Couples were classified into HDS > 15% group and HDS ≤ 15% group based on the HDS thresholds recommended by the manufacturer’s instructions. After controlling the bias between groups by the propensity score-matching method, the Mann-Whitney U test or Chi-squared test was used to evaluate the differences between groups. Regression analysis was used to assess the effect of HDS levels on fertilization, embryo quality, and clinical outcome of IVF cycles Main results and the role of chance No significant differences were observed between the HDS > 15% group and HDS ≤ 15% group regarding the number of fertilized oocytes (10.00 [6.00, 15.00] vs. 10.00 [6.00, 15.00], P = 0.230), the number of 2 pronuclei zygotes (8.00 [4.00, 12.00] vs. 8.00 [5.00, 12.00], P = 0.311), the number of cleaved zygotes (10.00 [5.00, 15.00] vs. 10.00 [6.00, 15.00], P = 0.301), and the number of high-quality embryos on day 3 (5.00 [2.00, 9.00] vs. 5.00 [3.00, 9.00], P = 0.729). However, linear regression analysis showed that HDS levels negatively impacted fertilization (adjusted B value = −0.015, 95% CI: −0.028 ∼ −0.002, P = 0.022) and 2 pronuclei formation (adjusted B value = −0.015, 95% CI: −0.029 ∼ 0.000, P = 0.046). The implantation rate (47.1% vs. 50.2%, P = 0.418), clinical pregnancy rate (60.9% vs. 64.5%, P = 0.440), ongoing pregnancy rate (83.7% vs. 86.7%, P = 0.475), early miscarriage rate (16.3% vs. 13.3%, P = 0.475), late miscarriage rate (1.1% vs. 3.5%, P = 0.232), and live birth rate (82.6% vs. 83.2%, P = 0.896) were not significantly different between groups. Linear regression analysis showed that HDS did not affect the implantation rate. Binary logistic regression analysis also showed that HDS did not affect clinical pregnancy, ongoing pregnancy, early miscarriage, late miscarriage, and live birth. Limitations, reasons for caution The main weakness of this study was the nature of the retrospective design, and additionally, patients were not randomized. Wider implications of the findings Although our results are not entirely new, it can be considered as reliable because 2604 IVF cycles and 548 fresh IVF-ET cycles were included and subsequently controlled the bias between groups This study suggested that HDS might be an indicator in predicting the fertilization ability of sperm in IVF treatment. Trial registration number not applicable