Short tandem repeat (STR) variation has been proposed as a major explanatory factor in the heritability of complex traits in humans and model organisms. However, we still struggle to incorporate STR variation into genotype–phenotype maps. We review here the promise of STRs in contributing to complex trait heritability and highlight the challenges that STRs pose due to their repetitive nature. We argue that STR variants are more likely than single-nucleotide variants to have epistatic interactions, reiterate the need for targeted assays to genotype STRs accurately, and call for more appropriate statistical methods in detecting STR–phenotype associations. Lastly, we suggest that somatic STR variation within individuals may serve as a read-out of disease susceptibility, and is thus potentially a valuable covariate for future association studies.