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Background: The available data on the relationship between diet/folic acid and congenital heart disease (CHD) are not consistent. This study aimed to investigate the relationship between the intake and supplementation of folic acid and other selected factors in mothers and the risk of congenital heart defects in fetuses. Methods: A case–control study was conducted. The study group included pregnant women with fetuses from singleton pregnancies with prenatally diagnosed heart defects in the fetus (n = 79) and pregnant women whose course of pregnancy was normal with no heart defects or other developmental anomalies diagnosed in the fetus (n = 121). The patients were diagnosed at a reference center in Poland. The women completed a lifestyle questionnaire and FFQ and precisely described their use of dietary supplements. A univariate logistic regression model was used to evaluate the association between folic acid and selected risk factors and CHD. The association was significant and included such risk factors such as nutritional status, medications taken, smoking, and alcohol consumption. Additionally, the time of starting folic acid supplementation turned out to be statistically significant. The reference period of supplementation was the period before pregnancy. Results: Lack of supplementation increases the risk of heart defects in children by more than four times compared to supplementation before pregnancy (OR = 4.19; p = 0.0117), whereas supplementation beyond the eighth week of gestation increases the risk almost threefold (OR = 2.90; p = 0.0474). The presence of congenital defects in the family is also an important factor. Conclusions: A history of congenital heart defects or other defects, lack of periconceptional folic acid supplementation, and lack of dietary supplementation before pregnancy were associated with congenital heart defects in the fetus. Place of residence, parents' education, lifestyle habits such as smoking and alcohol consumption, nutritional status before pregnancy, and mother's diseases did not show a significant relationship with congenital heart defects in the children. There is an urgent need to develop preventive strategies and conduct extensive public education. [ABSTRACT FROM AUTHOR]