Cilia play key roles in mammalian development and the ciliome (the set of genes encoding proteins involved in cilia formation and function) is thought to be well-conserved. However, ciliopathies are associated with a broad range of tissue-specific phenotypes. Here, Kevin Peterson, Samantha Brugmann and colleagues use bulk RNA-sequencing to compare ciliary gene expression across six distinct murine embryonic tissues. They find that around 29% of the ciliome is differentially expressed (DE) between these tissues, terming this the ‘DE ciliome’. Analysis of human protein sequences and embryo viability suggests that the DE ciliome is under less evolutionary constraint than the core ciliome, possibly because it contributes to tissue-specific differences rather than to essential ciliary processes. Comparing transcriptomic data from E11.5 neural crest cells and E13.5 skeletal progenitors reveals changes in ciliary gene expression, suggesting that the ciliome is dynamic, as well as spatially heterogeneous. Pcm1 and Tmem107 are significantly upregulated over this period and knocking out these genes in mouse embryos results in skeletal defects. Overall, this work identifies that cilia are heterogeneous organelles and begins to unpick the mechanisms underlying this variation. The data from this study represent a useful resource for other researchers in the field.