Genetic factors contribute to risk for many common diseases affecting reproduction and fertility. In recent years, methods for genome-wide association studies (GWAS) have revolutionised gene discovery for common traits and diseases. Results of GWAS are documented in the Catalog of Published Genome-Wide Association Studies at the National Human Genome Research Institute and report over 70 publications for 32 traits and diseases associated with reproduction. These include age at menarche, endometriosis, uterine fibroids, infertility, polycystic ovary syndrome, and cancers of the reproductive tract. Results that pass appropriate stringent levels of significance are generally well replicated in independent studies. Examples of genetic variation affecting twinning rate, infertility, endometriosis and age at menarche demonstrate that the spectrum of disease related variants for reproductive traits is similar to most other common diseases. GWAS “hits” provide novel insights into biological pathways contributing to disease risk and the translational value of these studies lies in discovery of novel gene targets for biomarkers, drug development and greater understanding of environmental factors contributing to these diseases. Results also show genetic data can help define sub-types of disease and co-morbidity with other traits and diseases. To date, many studies on reproductive traits have used relatively small samples. Future genetic marker studies in large samples with detailed phenotypic and clinical information will yield new insights into disease risk, disease classification and co-morbidity for many diseases associated with reproduction and infertility.