The aim of this study was to investigate the association between a history of prepregnancy obesity and a woman's future long-term risk for the development of female malignancies. A population-based study compared the incidence of long-term female malignancies in a cohort of consecutive women with and without a diagnosis of prepregnancy obesity. Deliveries occurred between the years 1988 and 2013, with a mean follow-up duration of 11.6 years. Women with known malignancies before the index pregnancy and known genetic predisposition for malignancy were excluded from the study. Female malignancies were divided according to specific type (ovary, uterine, breast, and uterine cervix). A Kaplan-Meier survival curve was used to estimate the cumulative incidence of malignancies. A Cox proportional hazards model was used to estimate the adjusted hazard ratios for female malignancy. During the study period, 106 251 deliveries fulfilled the inclusion criteria; 2.2% (n=2360) occurred in patients with a history of prepregnancy obesity. During the follow-up period, patients with prepregnancy obesity had a significantly increased risk for hospitalization because of female malignancies as a group and specifically ovarian and breast cancer. Using a Kaplan-Meier survival curve, patients with a previous diagnosis of prepregnancy obesity had a significantly higher cumulative incidence of female malignancies. Using a Cox proportional hazards model, adjusted for confounders such as gestational diabetes mellitus and maternal age, prepregnancy obesity remained independently associated with long-term risk for female malignancies (adjusted hazard ratio: 1.4; 95% confidence interval: 1.1-1.9; P=0.045). Prepregnancy obesity is an independent risk factor for long-term female malignancies such as ovarian and breast cancer.