In Drosophila, biogenesis of the major rhodopsin, Rh1, is dependent on the presence of a photoreceptor cell-specific cyclophilin, NinaA. In ninaA mutants, Rh1 is retained within the endoplasmic reticulum and rhodopsin levels are reduced > 100-fold. Cyclophilins have been shown to be peptidyl-prolyl cis-trans isomerases and have been implicated in catalyzing protein folding. We have generated transgenic animals expressing different functional rhodopsins containing a histidine tag. We isolated these molecules from wild-type and ninaA mutant retinas, and have demonstrated that in vivo NinaA forms a specific stable protein complex with its target Rh1. We also expressed ninaA under an inducible promoter and showed that NinaA is required quantitatively for Rh1 biogenesis. These results provide the first evidence for a biologically relevant physical interaction between a cyclophilin and its cellular target, and suggest that the normal cellular role of this class of cyclophilins is to function as chaperones, possibly escorting their protein substrates through the secretory pathway.