Mutations in the clk-1, clk-2, clk-3 and gro-1 genes in Caenorhabditis elegans show alterations in developmental and behavioral timing and lifespan, collectively termed the Clk phenotype. While the clk-1, clk-2, and gro-1 genes have been cloned, clk-3 gene has not been identified. Gene expression changes in clk-3 mutant worms were determined using microarray expression data. I examined genes in the region to which clk-3 gene maps, for strongly reduced expression in the clk-3 mutants and identified thirteen clk-3 candidate genes. RNAi feeding vectors for all these candidate genes were picked and cultured from the RNAi library. Knock-down worm strains were generated by feeding RNAi and analyzed for Clk phenotypes. Of all the candidate genes tested, the Y48E1B.5 gene showed the most similar phenotypic profile to the clk-3 mutants. The Y48E1B.5 gene shows weak homology to a mammalian mitochondrial ribosomal protein. Primers were designed to amplify all 9 exons of the Y48E1B.5 gene. Sequence analysis was carried out on the resulting PCR products from clk-3 mutants. An amino acid change was found in exon 4.