The timing of reproduction in birds varies considerably within populations and is often under strong natural selection. Individual timing within years is dependent on a range of environmental factors in addition to having an additive genetic basis. In vertebrates, an increasing amount is known about the molecular basis for variation in biological timing. The Clock gene includes a variable poly-glutamine (poly-Q) repeat influencing behaviour and physiology. Recent work in birds, fish and insects has demonstrated associations between Clock genotype and latitude across populations, which match latitudinal variation in breeding time. In this study, we investigated the phenotypic correlates of variation in Clock genotype within a single blue tit Cyanistes caeruleus population over two successive breeding seasons. In females, but not in males, we observed a general trend for birds with fewer poly-Q repeats to breed earlier in the season. Incubation duration was shorter in both females and males with fewer repeats at the polymorphic Clock locus. Poly-Q Clock allele-frequency was homogenously distributed within the study population and did not exhibit any consistent environment-related variation. We further tested for effects of Clock genotype on reproductive success and survival, and found that females with fewer poly-Q repeats produced a higher number of fledged offspring. Our results therefore suggest that (i) selection in females, but not in males, for fewer poly-Q repeats may be operating, (ii) the across–population associations in timing of breeding involving this locus could be linked to variation within populations, and (iii) the Clock gene might be involved in local adaptation to seasonal environments.