Stature and puberal timing are two complex genetic traits that vary widely within a population due to a combination of genetic and environmental factors. Rare mutations explain a fraction of severe short stature, but rare mutations are less likely to explain most of idiopathic short stature or most of the population variation in height or the timing of puberty. In this review, we discuss how association and linkage studies, in conjunction with new genomic technologies, will allow researchers to survey genes for the variants that underlie these traits. For both association and linkage studies to be successful, large samples and careful interpretation are critical.