The rapidly accumulating data of sequenced microbial genomes allows to conduct systematic studies on microbial gene regulation as well as function. As proteins are often the functional molecules, proteomics is particularly booming in the functional studied of microbial genomics. Using comparative studies as the powerful tools, a fundamental principle in microbial proteomics is to elucidate and to understand the gene expression levels in different microorganisms or under different growth conditions. It is very obvious that the quantitative analytical techniques are highly required for comparative proteomics. The current status of the approaches applied to quantitative analysis of microbial proteomics were reviewed.