Individual variation in the genetic constitution of humans may affect the host responses to constant assaults from exogenous and endogenous carcinogens, which will eventually impact cancer risk, disease prognosis and clinical outcome. Bladder cancer is one of the most common cancers in the world. In this review, the published research articles studying the association between genetic polymorphisms and bladder cancer risk and disease progression are summarized. Genetic polymorphisms are categorized based on their primary cellular functions: genes in carcinogen metabolism, DNA repair, cell cycle control, inflammation, apoptosis, methylation, genes functioning as G proteins, and cell adhesion molecules. Furthermore, we discuss a number of limitations of current genetic susceptibility research and suggest future directions in molecular epidemiology study. This review presents an overview of current molecular epidemiology of bladder cancer and provides a useful resource for understanding the pathogenesis of bladder cancer.