Background: Endometriosis is defined by the presence of endometrium outside the uterus. Changes in the expression of the proto-oncogene c- kit are associated with aggressive behaviour of both benign and malignant tumours, but there are few data on its c- kit expression in endometriosis. Here we examined c-kit expression in endometrium and endometriotic tissue. Methods: Immunohistochemistry was used for qualitative and semi-quantitative (mean ± S.D. positive cells) analysis of c-kit expression in endometrium from women with ( n = 9) and without endometriosis ( n = 18), and in peritoneal ( n = 20), ovarian ( n = 20) and colorectal endometriosis ( n = 20). Results: Semi-quantitative c-kit expression was higher in endometrial glandular cells from women with endometriosis than from women without endometriosis (15.0 ± 14.6% versus 3.9 ± 7.4%, p = 0.01). No difference in c-kit expression was found in qualitative analysis and according to the phase of the menstrual cycle. C-kit expression values in peritoneal, ovarian and colorectal endometriosis were 2.0 ± 3.8%, 2.0 ± 4.1% and 21.7 ± 18.4%, respectively. Qualitative and semi-quantitative c-kit expression was higher in colorectal endometriosis than in peritoneal and ovarian endometriosis ( p < 0.001); no difference was found between ovarian and peritoneal endometriosis. No c-kit expression was detected in stromal cells of either endometrium or endometriotic tissue. Conclusion: These results suggest that the c-kit/stem cell factor axis is involved in the pathogenesis of endometriosis. Strong c-kit protein expression was associated with invasive endometriotic lesions.