The dissection of the circadian clock into its molecular components represents the most striking and well-studied example of a gene regulatory network underlying a complex behavioural trait. By contrast, the evolutionary analysis of the clock has developed more slowly. Here we review studies that have surveyed intraspecific clock gene variation over large geographical areas and have discovered latitudinal clines in gene frequencies. Such spatial patterns traditionally suggest that natural selection shapes genetic variation, but it is equally possible that population history, or a mixture of demography and selection, could contribute to the clines. We discuss how population genetics, together with functional assays, can illuminate these possible cases of natural selection in Drosophila clock genes.