Little is known about the molecular determinants of ovarian cancer, the fifth most common cause of cancer death in women. CpG island (CGI) hypermethylation is known to turn off gene expression and is associated with cancer progression. Our group used differential methylation hybridization, a microarray-based technique, to scan for alterations in methylation in ovarian cancer. We performed such screening of stage IIIC epithelial ovarian carcinomas (N=10), normal ovarian surface epithelial cells and ovarian cancer cell lines. A wide range of hypermethylated CGIs (2.5-fold increase; P <0.05) was seen in the ovarian carcinomas (23–98); however, the number of hypermethylated CGIs was similar across ovarian cancer cell lines (38–51). There were 12 hypermethylated CGIs (P<0.05) common to the ovarian cancer cell lines and tumors. Sequencing analysis revealed 11 methylated CGI tags in the ovarian tumors that had previously been shown to be hypermethylated in breast cancer. Tumor methylation levels before therapy were associated with patient response to chemotherapy (P=0.048; one-sided exact Wilcoxon rank sum test). Patients displaying a complete response had tumors with a low methylation score; conversely, patients with progressive disease had tumors with a higher methylation score. Although we have analyzed only a small fraction (2%) of the CpG islands in the human genome, we have found a relationship between the amount of methylation in ovarian tumors and response to chemotherapy. Our proof-of-concept study lays the foundation for genome-wide screening of methylation using DMH to examine epigenotype-phenotype relationships in ovarian cancer.