Centrioles are intriguing cylindrical organelles composed of triplet microtubules. We used mass-spectrometry based MudPIT (multidimensional protein identification technology) to identify the protein composition of centrioles isolated from the green alga Chlamydomonas. This proteomic analysis was the first published centriole proteome and revealed orthologs of human ciliary-disease genes. We found that two classes of ciliary disease genes were highly represented among this centriole proteome: cystic kidney disease syndromes and cone-rod dystrophy syndrome genes. Further characterization of one highly abundant WD40 protein, POC1 (proteome of the centriole protein 1), demonstrated it's role in both centriole duplication and centriole length control. By identifying a parts list for the centriole, the centriole proteome has laid the foundation for studies centering around all aspects of centriole biology.