Endometriosis is one of the most common gynecological abnormalities. Endometriosis cyst in the ovary also exhibited changes in epithelial cyst just like endometrium in the uterus. Nowadays, there are some research that linked endometriosis and clear cell ovarian cancer which is known with endometriosis-associated ovarian carcinoma (EAOC). It is reported that there's a mutation that activated tumor suppressor gene (ARID1A), so protein BAF250a is not expressed in Clear Cell Carcinoma (CCC) in the ovarium. Immunohistochemistry staining of ARID1Awere done in 20 samples of non-atypical endometriosis, 20 cases of atypical endometriosis, 20 cases of CCC in the ovarium from 2012 until march 2015. From the CCC we get 9 cases of EAOC. After that, we see if there's any difference in the percentage of ARID1A expression in non-atypical, atypical endometriosis, CCC in the ovarium and endometriosis with CCC (EAOC). In non-atypical, atypical endometriosis and CCC groups there are significant differences on the percentage of ARID1A expression (Kruskal-Walis test p=0.0035). There are significant differences on ARID1Aexpression between non-atypical and atypical endometriosis with EAOC (p=0.001 and p=0.0015). In non-atypical, atypical endometriosis and CCC there are significant differences on the percentage of ARID1A expression (Kruskal-Walis test p=0.011). There are significant differences on ARID1Aexpression between non-atypical and atypical endometriosis with EAOC (p=0.005 and p=0.008). The expression of ARID1A in non-atypical and atypical endometriosis are significantly higher than ovarian CCC and EAOC. ARID1A may be used as a marker for malignancy transformation in endometriosis.