Background: In the multifactorial etiology of orofacial clefts (OFCs), environmental factors play an important role. To trace the influence of these factors, the timing of the cell biological mechanisms that occur during embryological development of the primary and secondary palates must be taken into account. That is, the fusion process of the facial and palatal processes, respectively, followed by their differentiation into bone and musculature, which take place during the first trimester of pregnancy. During this period, harmful seasonal influences such as viral infections and vitamin deficiencies could induce OFC in the embryo. Aims: The aim of this study is to find out whether a seasonal conception period with an increased risk of OFC development exists, particularly gender related. Methods: This was a retrospective cross-sectional study on children with OFC born in the Netherlands from 2006 to 2016. Total conception rates of live births in the Netherlands were used as a control group. χ2 tests were performed to analyze monthly and seasonal differences. Males and females, positive and negative family history and subphenotype groups based on fusion and/or differentiation (F- and/or D-) defects, and their timing in embryogenesis were analyzed separately. Results: In total, 1653 children with OFC, 1041 males and 612 females, were analyzed. Only males with FD-defects showed a significant seasonal variation with an increase in conceptions during spring, most often in May. Conclusions: Males with FD-defects showed a significant seasonal variation with an increase in conceptions during spring. No other seasonal trends could be demonstrated.