Technical Abstract: Background Growth and feed efficiency are key traits in selecting superior animals for genetic improvement programs. Fast, efficiently growing animals have increased protein synthesis and/or reduced protein degradation relative to slow, inefficiently growing animals. Microarray expression profiling allows for the detailed characterization of the genes/pathways that regulate processes of protein turnover. Results We evaluated changes in hepatic global gene expression in response to 3-week starvation in rainbow trout. Microarray analysis revealed a coordinated, down-regulated expression of protein biosynthesis genes in starved fish. In addition, genes of lipid metabolism/transport, aerobic respiration, blood functions and immune response were decreased in response to starvation. However, the microarray approach did not reveal a significant increase of gene expression in protein catabolic pathways. Further studies using real-time PCR and enzyme activity assays were performed to investigate the gene expression patterns of the major proteolytic pathways, cathepsins, calpains and the multi-catalytic proteasome. Feed restriction reduced mRNA accumulation of the calpain inhibitor, calpastatin (CAST), with a subsequent increase in the calpain catalytic activity. In addition, starvation caused a slight but significant increase in 20S proteasome activity without affecting mRNA levels of the proteasome genes suggesting a post-transcriptional action. Starvation did not affect activities or mRNA accumulation of cathepsin D and L. Conclusion These results suggest a significant role of calpain and 20S proteasome pathways in protein mobilization as a source of energy during fasting and a potential association of the CAST gene with fish growth efficiency.