There have been no large, nationwide, birth cohort studies in Japan examining the effects of house renovation during pregnancy on congenital abnormality. This study examined the impact of (1) prenatal exposure to house renovation and (2) maternal occupational exposure to organic solvents and/or formaldehyde on the incidence of congenital abnormality. The fixed data of 67,503 singleton births from a large national birth cohort study that commenced in 2011 were used to evaluate the presence of congenital abnormalities and potential confounding factors. We employed multiple logistic regression analysis to search for correlations between maternal exposure to house renovation or organic solvents and/or formaldehyde during pregnancy and such congenital abnormalities as congenital heart disease, cleft lip and/or palate, male genital abnormality, limb defect, and gastrointestinal obstruction. After controlling for potential confounding factors, we observed that house renovation was significantly associated with male genital abnormality (OR 1.81, 95% CI 1.03-3.17, P = 0.04) when stratified by congenital abnormality, with no other remarkable relations to house renovation or occupational use of organic solvents and/or formaldehyde during pregnancy. There were also significant correlations for maternal BMI before pregnancy, history of ovulation induction through medication, maternal diabetes mellitus/gestational diabetes mellitus, and hypertensive disorder of pregnancy with an increased risk of congenital abnormality. In conclusion, this large nationwide survey provides important information on a possible association of house renovation during pregnancy with congenital male genital abnormality which needs confirmation in future studies.