Abstract Study question How is the sexual functioning of newly diagnosed unexplained infertile couples and which factors are associated? Summary answer At least 25% of couples are at risk of sexual dysfunction. Sexual functioning is associated with age, infertility duration, sperm quality, personal and relational wellbeing. What is known already A large proportion of unexplained infertile couples have the ability to conceive naturally over time. Sexual functioning is important for natural conception rates, but infertility is associated with reduced sexual functioning. Surprisingly, sexual functioning and its risk-factors are still understudied in unexplained infertility. Knowing the risk factors for reduced sexual functioning would enable fertility specialists to timely diagnose, prevent or treat sexual dysfunction, and in this way improve natural conception rates. The current literature is mainly based on individual-level data, neglecting the fact that observations, such as sexual functioning, arising from couples are not independent. Study design, size, duration Cross-sectional digital survey data and medical chart factors, which also served as the baseline assessment of a randomized controlled trial (Pleasure&Pregnancy, trial registration number NTR5709), were subjected to a dyadic analysis followed by linear regression. A total of 700 heterosexual couples recently diagnosed with unexplained infertility in secondary or tertiary fertility clinics were addressed between 2016 and 2021. Participants/materials, setting, methods Heterosexual couples (female age 18-38 year) with unexplained infertility and who were able to have coitus were eligible. Sexual functioning was assessed with the Female Sexual Function Index (FSFI) and International Index of Erectile Function (IIEF). Determinants included demographic, lifestyle and diagnostic and wellbeing factors as assessed with the Hospital Anxiety and Depression Scale (HADS) and the Revised Dyadic Adjustment Scale (R-DAS). B represents the impact on sexual functioning when a factor changes 1 unit. Main results and the role of chance A total of 581 (83%) women and 478 (68%) men filled out questionnaires. Survey data and medical chart factors were available for 451 couples. About one in four women (24.3%) and one in fourteen men (7.3%) were at risk of respectively female sexual dysfunction and erectile dysfunction after fertility work-up. Couples had a mean coital frequency of 7 times per month (SD 2.7). Higher female and male sexual desire (B: 0.04, p<0.01 and B: 0.02, p<0.02) and satisfaction (B: 0.03, p<0.01 and B: 0.06, p<0.01), but not orgasm were significantly associated with increased coital frequency. Own age (B: -0.64), anxiety (B: -9.47), depression (B: -7.61) and relationship distress (B: -8.97), and partners’ relationship distress (B: -5.08) and total motility sperm count (B: -4.88) were associated with lower female sexual functioning. Own age (B: -0.17), anxiety (B: -5.03), depression (B: -3.65), relationship distress (B: -5.77), and partners’ age (B: -0.46) and relationship distress (B: -3.14) and couples’ duration of infertility (B: -0.24) were associated with lower male sexual functioning. Limitations, reasons for caution The study is prone to selection bias given the inclusion of couples seeking medical help, consenting to a RCT and were having coitus. Not all previous identified determinants of sexual functioning were studied due to factors as missing data, low case numbers or not being assessed in the Pleasure&Pregnancy RCT. Wider implications of the findings Clinicians advising couples with unexplained infertility to continue natural conception, need to be aware that at least 25% of couples are at risk of sexual dysfunction. Clinicians should consider risk factors of reduced sexual functioning, take a sexual anamnesis and advice sexual counselling and treatment if indicated. Trial registration number Baseline assessment of RCT (Pleasure&Pregnancy) with trial registration number NTR5709