Endometriosis is characterized by the ectopic implantation of endometrium on peritoneal surfaces. Angiogenic and growth factors may play a significant role in the pathogenesis of endometriosis. Midkine (MK) and pleiotrophin (PTN) are two related peptides associated with carcinogenesis and angiogenesis. To test the hypothesis that a higher expression of MK and PTN in ectopic and eutopic endometrium from women with endometriosis might favour increased angiogenesis and growth with subsequent ectopic implantation, we investigated PTN and MK expression by quantitative competitive PCR (QC-PCR) in endometrium from 30 women with severe, stages III and IV endometriosis and from 30 women without endometriosis. Total RNA was extracted and reverse transcribed into cDNA, and QC-PCR was performed to evaluate PTN and MK mRNA expression. Results were analysed by analysis of variance. Eutopic endometrium from endometriosis patients showed increased expression of MK and PTN mRNA compared with endometrium from normal women in the luteal phase (P < 0.05). MK and PTN mRNA expression in ectopic endometrium was significantly lower than that in eutopic endometrium from women with and without endometriosis (P < 0.05). Our results suggest increased MK and PTN expression may be related to the initiation of ectopic endometrial implants and peritoneal invasion.