Abstract Study question Can microfluidic sperm sperm selection (MFSS) contribute to isolating spermatozoa with higher genomic integrity and cryostress resistance, while retaining embryo developmental competence? Summary answer In comparison to conventional density gradient (DG), MFSS yielded a higher proportion of motile spermatozoa coupled with enhanced genomic integrity and resistance to cryostress. What is known already The cryopreservation of human spermatozoa has long been a cornerstone in reproductive treatments, serving as a pivotal method for preserving male fertility for several decades. Despite the unlimited storage time of cryopreserved semen specimens, the thawing process inevitably diminishes the number of viable spermatozoa. The implementation of a technique capable of enhancing the motility of spermatozoa cryopreserved would yield a higher proportion of gametes with higher kinetics and genomic integrity at thawing. Study design, size, duration Since 2017, 183 men underwent cryopreservation utilizing MFSS. Post-processing semen parameters, including Sperm Chromatin Fragmentation(SCF), and post-thaw motility were compared with a DG control(n = 1979). Additionally, post-thaw parameters for 30 men who had previously employed DG and subsequently adopted MFSS for semen cryopreservation were included. In 12 specimens, a paired analysis was carried out on a same ejaculate. Moreover, we explored pregnancy outcomes with MFSS-selected specimens in some men that underwent ART. Participants/materials, setting, methods Semen parameters were analyzed, and DG was performed according to WHO 2021 guidelines. MFSS was carried out following manufacture’s protocol (ZyMōt® Multi 850µL). Cryoprotectant (Test Yolk Buffer) was added to the final sample before being immersed in liquid nitrogen. A minute aliquot of the processed sample, cryopreserved separately, was thawed for post-thaw motility. TUNEL assay was used to measure SCF (≤ 15% normal threshold). Main results and the role of chance In this study, 1979 men (40.0±7y) underwent DG prior to cryopreservation, resulting in a 44.3±25x106/mL concentration, 88.2±4% motility, and 2.9±1% normal morphology, serving as control. The remaining 183 men of a similar age underwent MFSS prior to cryopreservation. Despite a lower concentration at 26.1±15x106/mL(P < 0.001), MFSS resulted in a higher post-processing motility(97.8±2%, P < 0.001) and normal morphology(3.4±1%, P < 0.001). Post-thaw analysis revealed a remarkably higher post-thaw motility in MFSS (51.2±7% vs 43.6%±4%,P < 0.001). SCF averaged 17%(raw), 11%(DG) and 2%(MFSS,P<0.001). To confirm research hypothesis, a pilot study was done in 12 men (37.3±3y,3.0±2d abstinence) with their semen specimen equally aliquoted for DG or MFSS and cryopreserved. The post-thaw motility increased from 45.4±8%(DG) to 61.3±13%(MFSS,P<0.001). Subsequently, in men(n = 30, 40.8±6y, 3.0±2d abstinence) who underwent semen cryopreservation previously by DG and subsequent by MFSS, a similar trend was observed with a higher post-thaw motility (53.2±6% vs 43.2%±6%,P < 0.001). Among the 36 patients who utilized DG cryopreserved specimen for reproductive purposes, 11/19 (57.9%) patients achieved pregnancy in ICSI cycles. while 5/17 (29.4%) achieved pregnancy in an IUI cycle, Among the 18 couples who used MFSS cryopreserved specimen for ICSI, a pregnancy rate was reported (8/18,44.4%). A IUI pregnancy rate was also reported (4/18,22.2%) using MFSS cryopreserved specimen. Limitations, reasons for caution While MFSS has proven to increase post-thaw survival rate and maintain a lower SCF, it did not necessarily trend in a higher pregnancy in IUI cycles, possibly due to the borderline elevated SCF. This finding needs to be confirmed in a larger population. Wider implications of the findings In reproductive medicine, we strive to identify new techniques aimed at providing more competent gametes. MFSS was capable of isolating the most motile potion of spermatozoa with a higher genomic integrity. The utilization of MFSS for specimens to be cryopreserved appears promising in generating higher post-thaw recovery of motile spermatozoa. Trial registration number not applicable