Substantial evidence shows that the heterogeneity of individual cells within a genetically identical population can be critical to their chance of survival. Methods that use average responses from a population often mask the difference from individual cells. To fully understand cell-to-cell variability, a complete analysis of an individual cell, from its live state to cell lysates, is essential. Highly sensitive detection of multiple components and high throughput analysis of a large number of individual cells remain the key challenges to realise this aim. In this context, microfluidics and lab-on-a-chip technology have emerged as the most promising avenue to address these challenges. In this review, we will focus on the recent development in microfluidics that are aimed at total single cell analysis on chip, that is, from an individual live cell to its gene and proteins. We also discuss the opportunities that microfluidic based single cell analysis can bring into the drug discovery process.