We have established earlier that rod photoreceptor cGMP-phosphodiesterase (PDE6) alpha and beta subunits are equally represented in the retina at the protein level and have similar turnover rates. mRNA quantification revealed five PDE6beta messages for every PDE6alpha transcript pointing at post-transcriptional regulation of PDE6alpha and PDE6beta expression. Indeed, the wild-type PDE6alpha mRNA was translated 5-fold more efficiently than that of PDE6beta. The coding regions of these subunits had a major contribution in this process. Here, we extend our study of translational regulation of PDE6 subunits and present a detailed analysis of the role of PDE6alpha and PDE6beta 5'- and 3'-UTRs (untranslated regions) in this process. We showed that both the short and long PDE6beta 5'-UTRs lead to more efficient protein synthesis than the PDE6alpha 5'-UTR. The 3'-UTRs of PDE6alpha and PDE6beta stimulated translation by approximately 2- and 3-fold, respectively. However, the positive effect of the PDE6alpha or PDE6beta 3'-UTRs was not observed when these regions were placed in constructs containing the 5'-UTR of the corresponding PDE6 subunit. Furthermore, it appears that PDE6alpha 5'- and 3'-UTRs may be involved in a base pairing interaction that reduces the efficiency of protein synthesis. Finally, using progressive deletion analysis of the PDE6alpha 5'-UTR, we have identified several regions that have significant contribution in regulation of protein synthesis. Based on these and earlier published data, it can be stated that an equimolar level of PDE6alpha and PDE6beta synthesized from different amounts of mRNA (ratio of PDE6alpha to PDE6beta mRNA in the retina is 1:5) is achieved as a result of combinatorial effects of 5'-UTRs and coding regions of PDE6alpha and PDE6beta mRNAs on translational regulation.