Different biotic agents such as bacteria, fungi, nematode and virus interact with plants, and causes significant annual crop loss. The plants interact with these pathogen and undergo various changes at physiological, biochemical and molecular levels. The omics technique is a powerful way which provides important information related to molecular changes occurring during plant-pathogen interaction. Several studies have been conducted and revealed either up or down-regulation of many genes involved in metabolism, energy, photosynthesis, signaling, defense and ROS upon pathogen interaction. In this review, we highlight recent progress in proteomic studies of plant-pathogen interaction, which could be useful for controlling disease and development of molecular markers for early detection of different diseases.