The aim of this prospective study is to define markers that can be used in the diagnosis and follow-up of patients with endometriosis by determining serum CA 125, transforming growth factor β1 (TGF-β1), interleukin 6 (IL-6), and IL-12 levels. The study group consisted of 14 patients diagnosed to have mild to moderate peritoneal endometriosis, 47 patients with ovarian endometrioma during laparoscopy and 12 healthy patients as a control group. Serum CA 125, TGF-β1, IL-6, and IL-12 levels were evaluated using ELISA kits. Serum CA 125 levels were significantly higher in the endometrioma group when compared to the control group (p < 0.001) and mild to moderate peritoneal endometriosis group (p < 0.001). Mean serum TGF-β1 levels were significantly higher in the endometrioma group when compared to the mild to moderate peritoneal endometriosis group (p < 0.001). In addition, serum TGF-β1 levels were found to be significantly different with regard to the stage of the endometriosis. Serum IL-6 levels were significantly higher in the endometrioma group compared to the endometriosis group (p = 0.024) and control group (p = 0.05). Mean serum IL-12 levels were lower in patients with endometriosis. In conclusion; TGF-β1 and IL-6 measurements might be a promising alternative in adjunct to CA 125 for the non-invasive diagnosis of endometrioma. However CA 125, TGF-β1, IL-6 and IL-12 seem not to have the diagnostic value in the diagnosis of early stage endometriosis. Of all the serum markers studied, only TGF-β1 was found to be correlated with the stage of endometriosis.