Objective: Sexual function is an important part of each human being’s personality and in the general couple relationship, with an obvious impact on quality of life and safe sexual performance during pregnancy is important for couples. The objective of this study was to assess effects of pregnancy on sexual function of couples. Materials: In a prospective cohort study 123 couples were enrolled in the study when women were first diagnosed to be pregnant. During their pre-natal visits, Sexual function of couples was evaluated using the Iranian Version Index of Erectile Function (IIEF) in men and Female Sexual Function Index (FSFI) in women in three trimesters. Statistical analysis was performed. Results: Indices of sexual function showed significant regressions over time during pregnancy. The greatness of the problem was highest during the third trimester. Female sexual arousal and sexual satisfaction domain scores had the major correlation to IIEF total score. On the other hand, male intercourse satisfaction domain score had the maximum correlation to FSFI total score. A strong correlation between male and female sexual function was observed. Conclusion: Sexual function is a widespread problem during pregnancy among Iranian couples. Therefore, pregnant women and their husbands need counseling about healthy sexual function in pregnancy.