With the development of microarray technology, and other whole genome approaches, it is now possible to systematically screen an entire genome for genes that are differentially expressed during two different stages of development and/or two different types of cells. This can be readily applied to muscle development by using genetic manipulations that either overexpress a key gene during development, or by using loss-of-function mutants. This chapter describes the genomic approaches that can be used to identify the vast majority (if not all) of the genes that are normally expressed in muscle cells, and can give an indication of their function during muscle development. These approaches include microarray analysis (transcriptome analysis), RNAi screens (phenome mapping), protein localization studies (localizome mapping), and protein-protein interaction studies (interactome mapping). As microarray analysis is the genomic approach that has been applied the most extensively to Drosophila muscle development, the main emphasis of this chapter will be on gene expression profiling during muscle development.