The physical and biological activity of any organisms is mainly depended on the genetic information which stored in DNA. A process at which a gene gives rise to a phenotype is called as gene expression. Analysis of gene expression can be used to interpret the changes that occur at biological level of a stressed cell or tissue. Hybridization technology helps to study the gene expression of multiple cell at a same time. Among them microarray technology is a high- throughput technology to study the gene expression at transcription level (DNA) or translation level (Protein). Analysis the protein only can predict the accurate changes that happens in a tissue, when they are infected by a disease causing organisms. Protein microarray mainly used to identify the interactions and activities of proteins with other molecules, and to determine their function for a system at normal state and stressed state. The scope of this chapter is to outline a detail description on the fabrication, types, data analysis, and application of protein microarray technology towards gene expression profiling.