Primary cilia play critical roles in many aspects of biology. Specialized versions of primary cilia are involved in many aspects of sensation. The single photoreceptor sensory cilium (PSC) or outer segment elaborated by each rod and cone photoreceptor cell of the retina is a classic example. Mutations in genes that encode cilia components are common causes of disease, including retinal degenerations. The protein components of mammalian primary and sensory cilia have not been previously defined. Here we report a detailed proteomic analysis of the mouse PSC complex. The PSC complex comprises the outer segment and its cytoskeleton, including the axoneme, basal body and ciliary rootlet, which extends into the inner segment of photoreceptor cells. The PSC complex proteome contains 1968 proteins represented by 3 or more unique peptides, including ~1500 proteins not detected in cilia from lower organisms. This includes 105 hypothetical proteins, and 51 proteins encoded by genes that map within the critical intervals for 22 inherited cilia-related disorders, increasing their priority as candidate genes. The PSC complex proteome also contains many cilia proteins not previously identified in photoreceptors, including 13 proteins produced by genes which harbor mutations that cause cilia disease, and 7 intraflagellar transport proteins. Analyses of PSC complexes from rootletin knockout mice, which lack ciliary rootlets, confirm that 1185 of the identified PSC complex proteins are derived from the outer segment. The mass spectrometry data, benchmarked by 15 well-characterized outer segment proteins, were used to quantify the copy number of each protein in a mouse rod outer segment. These results reveal mammalian cilia to be several times more complex than the cilia of unicellular organisms, and open novel avenues for studies of how cilia are built and maintained, and how these processes are disrupted in human disease.