Abstract Study question Does Spermocytogram parameters and Spermatozoa-DNA-Fragmentation (SDF) / Denaturation (SDD) levels are affected by atypical-bacterial semen infections in North-African men during the period between 2013-2022? Summary answer SDD presented positive-correlations with the presence of 3/5 atypical bacteria in the semen. Various Spermocytogram-parameters were also found to be negatively associated with atypical-bacterial-semen-infection. What is known already Atypical-Bacterial semen infections such as infections by Chlamydia-trachomatis (CT), Mycoplasma-hominis (MH) and genitalium (MG), Ureaplasma urealyticum (UU) and parvum (UP), were shown to be associated with poor sperm function (Prabha.et.al.,2009; Agarwal.et.al.,2012). In infections caused by CT, SDF was observed to be increased significantly and associated with male infertility (Karinen.et.al.,2004; Gallegos.et.al.,2008). In addition, MH and UU appeared to cause induction of nuclear decondensation and SDD, which damages sperm and has effects on sperm parameters. However, other studies failed to show any effect of MH, UU and CT on sperm parameters and SDD (Lee.et.al.,2013; Gdoura.et.al.,2008; Huang.et.al.,2015; Farsimadan and Motamedifar,2020). Study design, size, duration Retrospective study, including Sperm-culture-analyzes, Spermocytograms and SDF/SDD tests performed between January,2013 and December,2022 of 10.386 patients from North-Africa aged between 19 and 73 years-old (y.o) (average-age: 43.2 y.o ± 7.16). Patients were classified in 2 main groups according to the presence (Group-1: n = 613) or not (Group-2: n = 9773) of atypical-bacteria in the semen and 5 subgroups of monobacterial-infected-semen which were extracted from Group-1 as: CT (n = 14), MH (n = 61), MG (n = 10), UU (n = 147) and UP (n = 73) subgroups. Participants/materials, setting, methods 8201-Tunisian-patients(79%), 1142-Algerians(11%) and 1038-Libyans(10%) presented for semen-analyzes. Samples were analyzed according to World-Health-Organization (WHO) guidelines. Bacterial-semen-infection was detected by real-time-polymerase-chain-reaction(RT-PCR). Spermocytogram analyzes were performed according to WHO2010-recommendations using Sperm-class-analyzer-software (SCA5/6(CASA-system)) and SCA-scope (Microptic®). SDF analyzed with terminal-uridine-nucleotide-end-labeling(TUNEL)/sperm chromatin dispersion(SCD) techniques. SDD analyzed with the Aniline-Blue-staining-method. Statistical-analyzes were performed using SPSS22.0 for Windows-software. Kolmogorov–Smirnov-test for normality-analysis and comparisons by Student-t-test/Mann–Whitney U-test, as appropriate. Pearson/Spearman’ tests for correlations were used as appropriate, P-value<0.05 was considered as significant. Main results and the role of chance Sperm concentration was significantly lower in atypical-bacterial-semen-infected-group (Group-1) compared to controls (Group-2) with 11.39[0-311] vs 20.06[0-694]x106spz/mL, (p = 0.014); respectively, as well as progressive motility (14.6%[0%-64.47%] vs 21.89%[0%-81.35%], (p = 0.002); respectively) and typical morphology (5.34%[0%-18%] vs 9.29[0%-21%] (p < 0.001); respectively). However, Leucocytes concentration and SDD presented significant higher levels in Group-1 compared to Group-2 with 1.8[0.1-8.5] vs 0.5[0.1-2.45]x106 leucocytes/mL, (p < 0.001) and 21%[4%-60%] vs 15%[2%-75%], (p = 0.04); respectively. Similar significant differences were observed with 3/5 of the monobacterial-semen-infected-subgroups in comparison with Group-2 (MH, UU and UP-subgroups). No significant differences were observed in MG and CT-subgroups in except of SDD which presented significant higher levels in CT-subgroup in comparison with Group-2 (52%[4%-85%] vs 15%[2%-75%], (p = 0.002);respectively). Correlation-analyzes showed that SDD was positively correlated to MH (r = 0.069; p = 0.022) and UU (r = 0.084; p = 0.005) which is in accordance with the study of .Lee.et.al.(2013). Leucocytes concentration was also correlated positively to MH, CT, UU and UP (r = 0.047; p<0.001; r = 0.035; p=0.005; r = 0.074; p<0.001; r = 0.045; p=0.05; respectively). Sperm concentration, Progressive motility and Typical morphology presented Negative correlations with MH (r=-0.038; p=0.034; r=-0.048; p=0.05; r=-0.047; p=0.05; respectively), UU (r=-0.034;p=0.003; r=-0.04; p<0.001; r=-0.067; p=0.007; respectively) and UP (r=-0.072; p<0.001; r=-0.078; p=0.018; r=-0.057; p<0.05; respectively). Our results are in accordance with other studies such as of Prabha.et.al.(2009) and Agarwal. et al. (2012). However, SDF did not show any significant variation between our studied groups. Limitations, reasons for caution Our study is a retrospective-statistical survey that included patients presenting to the laboratory for fertility diagnosis or for a diagnosis due to a pathology and/or inflammation of the genital tract. Meta-analysis studies in addition to more prospective-randomized-controlled-trials in collaboration with IVF or other medical-analyzes-laboratories are necessary to confirm/refute our results. Wider implications of the findings These results should interest urologists, microbiologists, gynecologists, reproductive science fundamentalists, epidemiologists and embryologists who want to improve the investigations on the relationship between bacteria and semen parameters to the reasons of infertility, recurrent miscarriages and poor quality embryos in IVF. Trial registration number Not applicable