The overall purpose of this thesis project was to identify genetic mechanisms associated with differences in and regulation of feed intake and feed efficiency in pigs. The long-term goal of this research is to use this knowledge to improve feed efficiency in pigs, the largest variable cost in pork production, through genetic selection or management. The central hypothesis is that we can discover and characterize genetic pathways that control economically important traits related to feed intake and feed efficiency through transcriptional profiling of specific and relevant tissues during the growth period. Profiling studies were be based on two complementary animal-level contrasts and their interactions, including quantitative differences in a specific measure of feed efficiency, residual feed intake (RFI), and genetic differences for a candidate gene with known impact on feed intake and energy partitioning. In addition to the two profiling studies, we examined the effect of RFI selection on the thyroid axis as the thyroid hormones are critical component for growth and development of animals. We identified series of genes, pathways, and transcription factors that may underlie feed efficiency and feed intake in pigs using transcriptional profiling tools and specifically studied the thyroid axis and determined that the increased concentration of triiodothyronine that is peripherally produced may contribute to the decreased feed intake and increased efficiency observed in the low RFI pigs.