Abstract Study question Does sperm selection by a microfluidic sperm-sorting device improve laboratory outcomes of intracytoplasmic sperm injection cycles? Summary answer The ZyMōtTMdevice seems a good alternative to the conventional swim-up technique, possibly increasing progressive sperm motility post processing and blastulation rate. What is known already It is well-known that high levels of sperm DNA fragmentation negatively impact not only early embryonic development but also embryo genome activation. Microfluidic technologies for processing sperm samples selection such as the ZyMōtTM device have been developed to sort sperm with lower rates of sperm DNA fragmentation in order to improve in vitro fertilization (IVF) outcomes. Moreover, it offers several advantages: working with very small volume samples, high sensitivity and low reaction times, automatic sample treatment and analysis, among others. However, the real benefits on the clinical and laboratory outcomes of IVF cycles is yet to be determined. Study design, size, duration We performed a retrospective study including 126 seminal samples processed between May 2019 and December 2020. These samples belong to 63 infertile couples that underwent 2 consecutive IVF cycles using the swim-up technique in the first cycle (n = 63) and the ZyMōtTM device in the second (n = 63). The oocytes of the female partners were recovered and inseminated, and the embryonic culture was carried out until the blastocyst stage, when the quality of these embryos was analyzed. Participants/materials, setting, methods: A total of 118 seminal samples from 59 couples were included. Four couples were excluded due to insufficient seminal volume / concentration (2) or absence of mature oocytes recovered (2). Laboratory outcomes were evaluated including semen parameters post processing, as well as fertilization, cleavage, blastulation (blastocyst among cleavage stage) and top-quality blastocyst rates. Continuous variables were analyzed by paired Student’s t-test or Wilcoxon signed-rank test, as appropriate. Differences were considered significant when p-value < 0.05. Main results and the role of chance We did not find any difference in the percentage of non-progressive sperm motility [0 (0–33%) vs. 0 (0–10%); p = 0.063] and immotile sperm [0 (0–70%) vs. 0 (0–80%); p = 0.095] post processing when comparing the swim-up technique with the ZyMōtTM device. Likewise, no significant differences were detected regarding fertilization [83% (0–100%) vs. 89% (0–100%); p = 0.104] and cleavage [100% (0–100%) vs. 100% (80–100%); p = 0.217] rates in both groups. Nevertheless, there was a significant difference in the percentage of progressive sperm motility [100% (20–100%) vs. 100% (10–100%); p = 0.012] post processing, as well as blastulation [37% ± 0.32 vs. 50% ± 0.3; p = 0.031] and top-quality blastocyst [13.5% (0–100%) vs. 33% (0–100%); p = 0.009] rates, favoring the ZyMōtTM device. Limitations, reasons for caution The retrospective design and the small sample size make the study prone to bias. Furthermore, we do not have data on sperm DNA fragmentation pre and post processing. Clinical outcomes were not evaluated due to insufficient statistical power, since embryo transfer has not yet been accomplished in several patients. Wider implications of the findings: Besides the ZyMōtTM device has been indicated as a new tool to potentially improve laboratory and clinical IVF outcomes, it offers the advantage of being safe, fast, easy-to-use and less influenced by human errors. Further well-designed prospective studies are needed to prove its cost-effectiveness. Trial registration number Not applicable