We investigated the influence of pelvic endometriosis and ovarian endometrioma on pregnancy outcome in women associated with infertility. A total of 237 women with endometriosis were reviewed, and their fertility rate was assessed by both r-AFS staging and TOP classification as previously proposed by our group. There was no significant difference in pregnancy rate among r-AFS stages. However, the pregnancy rate was mostly affected by the tubal condition according to the TOP classification as follows: no adhesive lesion (T0), 53% (69/129); unilateral lesion (T1), 46% (18/39); bilateral lesion with at least one tube patent, (T2), 37% (10/27); bilateral tubal occlusion (T3), 0% (0/8) (p < 0.05, Mantel-Extension test). The absence (O0-O1) or co-existence (O2-O3) of ovarian endometrioma and different gradings of cul-de-sac obliteration (P2-P3) showed no significant differences in pregnancy rate. The resulting conception rate was also not affected by the size or location of ovarian endometrioma. In addition, the higher adhesion score of ovarian endometrioma involving the fallopian tube and as described in r-AFS classification had a significant detrimental effect on fertility. These observations suggest that our TOP classification describing individual tubal condition has a clinically predictive value in assessing the reproductive outcome of women with endometriosis.