Abstract Study question Does sperm affect the implantation and early embryogenesis? Summary answer Deranged sperm genomic integrity, limited repair mechanisms, aberrant gene expression have the potential to be transmitted to developing embryo and affect implantation and embryonic development. What is known already The terminally differentiated, transcriptionally quiscent sperm cells are vulnerable to a host of factors which might affect its function. The spermatozoa with truncated repair mechanisms have the potential to fertilize the oocyte, but eventually result in high rates of pre and post implantation losses. Oxidative stress, deranged genomic integrity, aberrant gene expression in the sperm cell has the potential to affect fertilisation potential, implantation and embryonic viability. This has been seen to be correlated with decreased fertilisation, clevage rates and blastocyst development and thus impaired implantation rates. Study design, size, duration A case control study of 75 men from infertile couples who had recurrent implantation failure (RIF) in IVF cycles and 75 fertile controls at AIIMS, New Delhi, India. Study duration was 2 years. Participants/materials, setting, methods Semen samples from men from couples who had RIF were analyzed as per WHO 2010. Sperm reactive oxygen species (ROS) and DNA fragmentation index (DFI) was assessed by chemiluminiscence and sperm chromatin structure assay (SCSA) respectively. Relative sperm telomere length was evaluated from sperm DNA by q-PCR analysis. The expression of genes pertinent for early embryonic development was done by qPCR. The relative quantification was done after normalizing with GAPDH and β-actin by 2-ΔΔCt method. Main results and the role of chance Seminal ROS levels (RLU/sec/million sperm) were seen to be significantly higher [57.75 (10.1-1186.9)] in cases with respect to controls [16.7(1.15-53.9)] (p < 0.001***). The mean DFI of men undergoing ART was significantly higher (37.7 ± 5.7) vs 23.2 ± 4.6%; p < 0.001***) in cases as compared to controls. ROS and DFI levels correlated negatively with sperm concentration and progressive motility (p < 0.001***). We analyzed the expression of FOXG1, SOX3, STAT4, RPS6, RBM9, RPL10A, RPS17, RPL29, WNT5A, HSP90, TOMM7, EIF5A genes. The expression of SOX3, RBM9, WNT5A, HSP90, TOMM7, and EIF5A showed a significant difference from control levels. The relative sperm telomere length was found to be significantly lower in RIF patients as compared to controls (p < 0.001***). Limitations, reasons for caution The current study was a case control study and lacked randomization and also is limited by low sample size. There is a lack of stratification in the enrollment of participants due to difference in specific risk of occurrence and varied clinical history. Wider implications of the findings The analysis of spermatozoal gene expression is important for understanding the sperm differentiation, fertilization and early embryonic events. Correlation with oxidative stress, genomic integrity and telomere length may help in regulationof gene expression. It may help in establishing sperm gene expression as a potential biomarker. Trial registration number Not applicable