There is a general belief that pregnancy has a beneficial effect on endometriosis but evidence is scanty. Moreover, some recent warning reports documented progression-growth of ovarian endometriomas during pregnancy. To further elucidate this aspect, we set up a prospective cohort study. We recruited 24 women carrying endometriomas at the time of in vitro fertilization who got pregnant. Selected women were contacted about 12-18 months after oocyte retrieval and invited to refer for ultrasound. The primary aim was to evaluate the modifications of endometriotic cysts after pregnancy. Twenty-four women carrying 40 endometriomas accepted to participate. The number of cysts per patient was significantly reduced following pregnancy (p = 0.003). It was unchanged in eight cases (33%), increased in two cases (8%) and reduced in three cases (13%). In the remaining 11 women (46%), no cyst could be detected. A comparison of the size of the endometrioma could be done in 21 cysts; the mean ± SD diameter before and after pregnancy was 20 ± 9 and 18 ± 7 mm, respectively (p = 0.27). In conclusion, pregnancy has a beneficial effect on endometriomas. A consistent proportion of cysts becomes undetectable after delivery. Further studies are warranted to clarify the mechanisms determining the disappearance of these cysts.