Current evidence on congenital malformations in the offspring of cancer survivors is largely inconsistent. Therefore, through this study we aimed to explore the prevalence of congenital malformations in the offspring of cancer survivors. To this end, female cancer survivors were identified from the Swedish Cancer Register and were further linked to the Swedish Medical Birth Register and Hospital Discharge Register to identify congenital malformation in their children at birth or during adulthood between 1987 and 2010. Multivariate logistic regression was used to estimate odds ratios and 95% confidence intervals for the association between congenital malformation and maternal cancer diagnosis. A total of 816 congenital malformations were noted among 9266 children of maternal cancer survivors, and the rate was 8.8%, whereas the rate in the general population was 7.7%. After adjusting for some confounding factors, we found that the risk for congenital malformation in children of cancer survivors was significantly increased with an odds ratio of 1.11 and 95% confidence interval of 1.04–1.20 as compared with that in controls. The increased risk was largely consistent irrespective of maternal age at diagnosis of cancer. The risk for congenital malformation was increased among offspring of female cancer survivors, which calls for further attention directed toward those cancer survivors who plan to have children.