Our pathway-based analysis of a large bladder cancer GWAS using two complementary pathway-based methods (GSEA and ARTP) identified an overrepresentation of association signals in seven pathways (‘Aromatic amine metabolism’, ‘NAD biosynthesis’, ‘NAD salvage’, ‘Clathrin derived vesicle budding’, ‘Lysosome vesicle biogenesis’, ‘Retrograde neurotrophin signaling’, and ‘Mitotic metaphase/anaphase transition’) and suggest involvement in at least three cellular processes (metabolic detoxification, mitosis, and clathrin-mediated vesicles). The gene discussed is BDNF; the disease is urinary bladder cancer.