Mutations in transition zone genes change the composition of the ciliary proteome. We isolated new mutations in RPGRIP1L (RPG1) that affect the localization of the transition zone protein NPHP4 in the model organism, Chlamydomonas. NPHP4 localization is not affected in multiple new IFT mutants. We compared the proteome of cilia from wild- type and mutants that affect the transition zone (RPGRIP1L) or intraflagellar transport (IFT172 and DHC1b) by mass spectrometry. The rpg1-1 mutant cilia show the most dramatic increase in cytoplasmic proteins. These nonciliary proteins function in translation, membrane remodeling, ATP production and as chaperonins. These proteins are excluded in isolated cilia from fla11-1 (IFT172) and fla24-1 (DHC1b). Our data support the idea that RPGRIP1L but not IFT acts as part of the gate for cytoplasmic proteins. The rpg1-1 cilia lack only a few proteins, which suggests only a small role of RPGRIP1L in the retention of ciliary proteins. The fla11-1 mutant shows the greatest loss/reduction of proteins, and one-third of these proteins have a transmembrane domain. IFT172 may play a role in the retention of proteins.