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OBJECTIVE: the aim of the present study was to verify whether there is a correlation between the prevalence of the polymorphism in the progesterone receptor gene named PROGINS and pelvic endometriosis at different stages. METHODS: a case-control study carried out from November 2003 to May 2004. The genotypes of 104 women were analyzed 66 women had had surgically confirmed endometriosis (26 women at stages I-II and 40 at stages III-IV), and 38 were healthy women. The 306-base pair Alu insertion polymorphism in the intron G of the progesterone receptor gene was detected by polymerase chain reaction and analyzed on 2% agarose gel stained with ethidium bromide. ANOVA analysis was performed in order to make comparisons between among the studied groups. RESULTS: the groups of women with endometriosis stages I-II (EndoI group) and stages III-IV (EndoII group) showed statistically significant increased incidence of PROGINS polymorphic allele as compared with the control group: 27% in the EndoI group, 38% in EndoII and 18% in the control group (p < 0.001. In the analyses, a high frequency of the PROGINS insertion was observed in women with endometriosis as compared to healthy women, disregarding the clinical stage of the disease (p = 0.0385). CONCLUSION: there is a significant statistical association between the PROGINS polymorphism and pelvic endometriosis.