Nucleotide diversity of the human Y chromosome is much lower than that in the rest of the genome. A new hypothesis postulates that this invariance may result from mutations in maternally inherited mitochondrial DNA (mtDNA), leading to impaired reproduction among males and lowered male effective population size. If correct, we should expect to see low levels of polymorphism in the male-specific Y chromosome of many organisms but not necessarily in the female-specific W chromosome in organisms with female heterogamety. However, recent observations from birds suggest that the avian W chromosome is very low in nucleotide diversity. This indicates that mtDNA mutations cannot broadly explain the evolution of the sex-limited chromosome. Other work has suggested that sexual selection at loci involved in sex determination or secondary sexual characteristics might reduce levels of genetic variability on Y through hitch-hiking effects. Although the W chromosome does not seen to play a dominant role for sex determination in birds, it cannot be excluded that selective sweeps arising from natural or sexual selection contribute to the low levels of genetic variability seen on this chromosome. BioEssays 25:163–167, 2003. © 2003 Wiley Periodicals, Inc.