Objective: Monthly variation in the total prevalence of the univentricular heart (UVH) and dextrotransposition of the great arteries (d-TGA) at gestational age 7 + 0 weeks was assessed to determine potential environmental factors, such as viral or bacterial infections, underlying the variation. Study design: The nationwide retrospective ten-year population-based cohort consisted of 592 733 births and 2764 terminated pregnancies due to fetal anomaly. The pre-or postnatally diagnosed cases of UVH (n = 440) and simple d-TGA (n = 127) from five national registers included live births, stillbirths, and pregnancy terminations due to fetal anomaly. We evaluated the variation in the monthly total prevalence of UVH and d-TGA at gestational age 7 + 0 weeks. The monthly variation of UVH and d-TGA was also compared with monthly variation in reported viral and bacterial infections. Results: In the UVH and d-TGA, we observed significant monthly variation in total prevalence. However, we observed no correlations in the studied viral or bacterial infections and the number of cases. Conclusions: Assessing monthly variation in total prevalence at early pregnancy, including pregnancy terminations and stillbirths, and using first-trimester timing provides the most accurate information on the variation. The reasons for monthly variation remain unclear, but we observed no associations with specific viral or bacterial infections.