BackgroundChildren conceived with assisted reproductive technologies (ART) or after a long waiting time have a higher prevalence of congenital malformations, but few studies have examined the contribution of type of infertility.ObjectivesTo quantify the association between causes of infertility and prevalence of malformations.MethodsWe compared the prevalence at birth of all and severe malformations diagnosed up to age 2 between 6656 children born in 1996–2017 to parents who had previously been assessed for infertility a an academic fertility clinic (“exposed”) and 10,382 children born in the same period to parents with no recent medical history of infertility (“reference”). We estimated prevalence ratios (PR) and prevalence differences (PD), by infertility status, type of treatment (non‐ART, ART), and infertility diagnosis, in all children and among singletons.ResultsCompared with children of parents with no infertility, children of parents with infertility had a higher prevalence of malformations (both definitions), particularly following ART conceptions. After accounting for treatment, ovulatory disorders were associated with a higher prevalence of both all (PR 1.49, 95% confidence interval (CI) 1.15, 1.93; PD 3.8, 95% CI 1.0, 6.6) and severe (PR 1.53, 95% CI 1.02, 2.29; PD 1.8, 95% CI −0.2, 3.7) malformations (the estimates refer to exposed children conceived without treatment). Unexplained and male factor infertility were associated with all and severe malformations, respectively. Estimates among singletons were similar. A diagnosis of ovulatory disorders was associated with all malformations also in analyses restricted to exposed children, regardless of treatment (we did not examine severe malformations, due to limited power).ConclusionsIn this study, ovulatory disorders were consistently associated with a higher prevalence of congenital malformations (including severe malformations) among live births, regardless of mode of conception.