Earlier age at menarche is related to shorter adult stature in large epidemiological studies35. We found that several adult height-increasing alleles were also associated with age at menarche (Table 3), but at different loci these alleles were associated with either earlier or later menarche. These paradoxical associations suggest a complex inter-play between growth and pubertal timing. Earlier menarche is associated with taller, rather than shorter, childhood height, and there are likely separate causal effects of rapid linear growth on earlier puberty, and of earlier pubertal maturation on earlier growth plate fusion and cessation of growth.