Osteoarthritis has a considerable heritable component, with GWAS variants residing in non-coding sequences near chondrocyte genes; loci which likely became evolutionarily optimized during bipedal knee formation. To explore this relationship, we epigenetically profiled joint chondrocytes, revealing evidence of selection and constraint on human knee-specific regulatory elements. These elements also overlap osteoarthritis loci, with risk variants contributing to disease heritability by altering constrained sequences. Using these findings we then describe a causal enhancer variant present in half the world’s population, showing that it impacts mouse knee-shape and osteoarthritis. Overall, our methods link an evolutionarily novel aspect of anatomy to its pathogenesis.