Abstract Study question Do the in vitro motility characteristics of sperm collected using a microfluidic device (ZyMot) differ from those of sperm collected by density gradient centrifugation (DGC)? Summary answer ZyMot-collected sperm had longer-lasting motility than those collected by DGC, but the head beat-cross frequency was inferior due to the absence of washing in vitro. What is known already ZyMot (DxNow, Inc., USA) can sort highly motile sperm with low reactive oxygen species (ROS), and DNA damage, without centrifugation. In IUI cycles, although the total number of ZyMot collected sperm was lower than that of DGC, it was reported that the pregnancy rate of ZyMot cycles was higher than that of DGC cycles. Washing sperm with a medium is essential for in vitro capacitation; however, the protocol for microfluidic devices lacks this procedure. The aim of this study was to clarify the motility characteristics of ZyMot-collected sperm. We also examined how washing ZyMot-collected sperm affected motility. Study design, size, duration The specimens were provided by patients who underwent semen analysis between October 2022 and January 2023, with written consent. We used 12 samples with a semen volume of 2.5 ml or more, or a motile sperm concentration of 4 million/ml or more. The same donor samples were divided into three groups (DGC, ZyMot, and ZyMot with wash). Dunnett’s test was performed with the DGC group as the control group. Participants/materials, setting, methods In the DGC group, 2-layer DGC (400G, 20 min) was performed, followed by washing (400G, 5 min). In the ZyMot group, ZyMot was used according to the manufacturer’s protocol. In the ZyMot with wash group, ZyMot-collected sperm was centrifugally washed (300G, 5 min). All samples were cultured at 30 °C until motility analysis. Sperm motility was analyzed using a computer-assisted sperm analysis system (SMAS) after 0, 4, and 24 h of semen preparation. Main results and the role of chance There was no significant difference in the motility rate of the two ZyMot groups compared to that of the DGC group at 0 and 4h after sperm preparation. On the other hand, the motility of the ZyMot group tended to be higher (53.3%, p = 0.0787), and the motility of the ZyMot with wash group was significantly higher (85.4%, p < 0.001) than that of the DGC group (33.5%), after 24h of sperm preparation. The straight-line velocity, curvilinear velocity, and average speed of the ZyMot and ZyMot with wash group did not differ from those of the DGC group at 0 and 4h. All speed parameters of the ZyMot with wash group were significantly higher than those of the DGC group, after 24h of culturing. Regarding sperm head movement, there was no significant difference in the amplitude of lateral head displacement between the two ZyMot groups compared to that of the DGC group at 0 and 4h of culture. In contrast, the sperm head beat-cross frequency of the ZyMot group was lower than that of the DGC group (9.18±0.31 Hz vs 8.71±0.49 Hz, p = 0.0409). Both head movement parameters of the ZyMot with wash group were significantly higher than those of the DGC group. Limitations, reasons for caution We chose semen samples with a high number of motile sperm because we divided the sperm into three experimental groups. Therefore, it is unclear whether our findings are applicable to patients with poor semen parameters. Wider implications of the findings ZyMot may be advantageous for IUI cycles because ZyMot-collected sperm maintains sustainable motility for extended periods. Alternately, ZyMot may be unfavorable compared to DGC in conventional IVF cycles due to inferior sperm head movement, which is a marker of capacitation. However, this disadvantage can be overcome by washing. Trial registration number not applicable