Abstract Study question Are chromosomal abnormalities (aneuploidy and mosaicism) increased in couples with unexplained infertility? Summary answer Couples with unexplained infertility show higher rates of embryo aneuploidy compared to IVF with donor sperm cycles. What is known already Aneuploidy is the most common genetic abnormality found in early embryos. Although there is strong evidence about the correlation between oocyte age and aneuploidy rates, the potential contribution of additional female and male factor warrants further elucidation. Unexplained infertility is a diagnosed of exclusion affecting ∼30% of couples seeking infertility care. Recent medical evidence suggests that these couples have lower odds of having a live birth compared to their counterparts using donor sperm. Therefore, the aim of this study was to elucidate whether chromosomal abnormalities (aneuploidy and mosaicism) were increased in couples with unexplained infertility. Study design, size, duration Retrospective analysis of the chromosomic evaluation of 700 embryos coming from 220 IVF/PGT-A cycles (March 2017 - September 2021) performed in a private fertility center. The comprehensive chromosome screening included testing for aneuploidy and mosaicism. In addition, whole and segmental chromosomal alterations were also identified and reported. Participants/materials, setting, methods Participants were divided into two groups: couples with unexplained infertility (study group) and women undergoing IVF using donated sperm (control group). Only normospermic and normal sperm FISH samples were included. The Veriseq NGS (Illumina) platform was employed for PGT-A testing. An SPSSv20.0 logistic regression analysis was performed for aneuploidy and mosaicism rate. The resulted odds ratio was then adjusted to account for: female/male age, previous implantation failure, recurrent pregnancy loss, previous chromosomopathies and embryo quality. Main results and the role of chance A total of 220 PGT-A cycles were included in the analysis (study group n = 94 vs control group n = 126) comprising 700 embryos (study group n = 313 vs control group n = 387). The female age was 38.17 ± 3.6 vs 40.08 ± 2.4 and the male age was 40.57 ± 5.0 and 25.37 ± 3.8, in the study vs control groups, respectively. Unexplained infertility couples showed a higher risk for generating aneuploid embryos compared to IVF with donor sperm cycles [OR = 2.33 IC 95% (1.11-5.00)]. In addition, whole chromosomal alterations [OR = 2.11 IC 95% (1.00-4.44)] as well as segmental chromosomal alterations rate [OR = 1.38 IC 95% (0.49-3.86)], were higher in unexplained infertility couples, but without reaching statistical significance. Regarding to mosaicism rate, no significant differences were found between groups: overall [OR = 0.74 IC 95% (0.30-1.83)], whole chromosome [OR = 0.92 IC 95% (0.35-2.46)] and segmental chromosomal [OR = 0.36 IC95% (0.10-1.34)] mosaicism. Limitations, reasons for caution The inherent limitations of a retrospective analysis. Additional studies are warranted to clarify the potential factors explaining the higher embryo aneuploidy risk in this sub-set of patients. Wider implications of the findings Our data suggest an increased risk for embryo aneuploidy in unexplained infertility couples undergoing ART. Since the treatment for these couples is largely empirical, our results emphasize the importance of PGT-A analysis as a potential strategy for unexplained infertility patients. Trial registration number Not applicable