Abstract Background Congenital heart diseases (CHDs) are the most common congenital anomaly. The causes of CHDs are largely unknown, but intrauterine mechanisms appear to be important. Higher prenatal body mass index (BMI), smoking and alcohol consumption are associated with increased risk of CHDs. Whether these are causal is unclear. Methods Seven European birth cohorts including 232,390 offspring were included. We applied negative exposure paternal control analyses to explore the intrauterine effects of maternal BMI, smoking and alcohol consumption during pregnancy, on offspring CHDs and CHD severity. We used logistic regression and combined estimates using a fixed-effects meta-analysis and compared maternal-specific confounder-adjusted associations to similarly adjusted associations of paternal exposures. If there is a causal intrauterine effect of a maternal pregnancy exposure, we would expect to see a maternal-specific association, with no (or weaker) association with the paternal exposure. Results There were 2,469 CHD cases (1.1%). The association of mean BMI with CHD was null and similar in mothers (adjusted OR per 1kg/m2: 1.00 (95%CI: 0.99, 1.02)) and fathers (OR: 1.01 (0.99, 1.03)). The analyses of BMI categories resulted in similar increased odds of CHD in overweight (mothers OR: 1.15 (1.01, 1.31) and fathers 1.10 (0.96, 1.27)) and obesity (mothers OR: 1.12 (0.93, 1.36) and fathers 1.16 (0.90, 1.50)). Maternal smoking was associated with increased odds of CHD (OR: 1.11 (0.97, 1.25)) but paternal smoking was not (OR: 0.96 (0.85, 1.07)). The difference increased when removing offspring with genetic/chromosomal defects (mothers OR: 1.15 (1.01, 1.32) and fathers 0.93 (0.83, 1.05)). The positive association with maternal pregnancy smoking appeared to be driven by non-severe CHD cases (OR: 1.22 (1.04, 1.44)). Associations with maternal (OR: 1.16 (0.52, 2.58)) and paternal (OR: 1.23 (0.74, 2.06)) moderate/heavy pregnancy alcohol consumption were similar. Conclusions We have shown that maternal, but not paternal, pregnancy smoking is associated with an increase in odds of offspring CHDs, primarily non-severe CHDs, providing evidence of an intrauterine effect. We found no strong evidence of an intrauterine effect of higher maternal BMI or alcohol consumption on offspring CHDs. Our findings provide further evidence for why smoking cessation is important during pregnancy.