Peritoneal endometriosis (PE) and deep endometriotic nodules (DEN) are gynecological diseases recently shown to be associated with elevated serum concentrations of organochlorines. The objective of the present study was to compare risk factors associated with both forms of the disease, with a particular attention to potential sources of organochlorine exposure. This matched case-control study with prospective recruitment included 88 triads (PE-DEN-control). All women were face-to-face interviewed with a standardized questionnaire, and serum dioxin and polychlorinated biphenyl measurements were available for 58 of them. Alcohol consumption (odds ratio (OR): 5.82 [confidence interval at 95% (95%CI) 1.20-28.3]) in DEN and low physical activity at work for DEN (OR: 4.58 [95%CI 1.80-11.62]) and PE (OR: 5.61 [95%CI 1.90-16.60]) were traced as significant risk factors. Organochlorine-related factors (use of tampons, occupational or environmental exposure) were not related to the disease. The current consumption of foodstuffs that were more likely to contribute to organochlorine body burden did not differ among the groups. Only some of these fatty foodstuffs (marine fish, pig meat) were traced by multiple regression analysis as significant determinants of organochlorine body burden, explaining only a small fraction (20%) of the interindividual variation of organochlorine body burden. We conclude that PE and DEN share similar patterns of risk or protective factors.