Combined oral contraceptive pill (COCP) lowers the risk of ovarian cancer. The risk reduction has been reported as between 33 - 41%. The duration of use affects the risk reduction. The mechanism of risk reduction has been theorised. According to the incessant ovulation theory, repeated ovulation causes inflammation, which causes mutations and subsequent carcinogenesis. COCP prevents ovulation, reducing cancer risk. It was previously shown that COCP decreased genome-wide CpG methylation, suggesting that COCP could regulate gene expression through epigenetic mechanisms. This study hypothesised that COCP intake would affect CpG methylation depending on tissues. It was hypothesised that differential CpG methylation was linked to differential gene expression, which could in turn affect tissue organisation. Reduced representation bisulphite sequencing (RRBS) and pyrosequencing were used to measure the methylation in mice. RNA sequencing (RNAseq) and quantitative reverse transcription PCR (RT-qPCR) were used to study gene expression. Haematoxylin & eosin (H&E) staining and light microscopy were used to detect changes in tissue organisation. Hypomethylation was observed across the genome. CpGs were differentially methylated in COCP treated mice compared to untreated mice. RNAseq revealed that COCP treatment for 5 weeks altered gene expression. In several genes, epigenetic changes were linked to altered gene expression. Subsequent RT-qPCR validated these findings, shown by up-regulation of Kallikrein 1 (KLK1) and fibroblast growth factor (FGF7). There were alterations in the number of ovarian follicles and tissue structures, with a significant change in antral follicle count. In conclusion, COCP changed CpG methylation and gene expression in mice. This was the first study which investigated the effect of COCP in the fallopian tubes. Future studies may build on the fallopian tube specific gene expression and investigate what roles they play in protection against ovarian cancer.