It is well established that individual cells, even from the same origin, differ from each other in many aspects due to stochastic biological processes and differences in environmental perturbations. Cell heterogeneity has been found to play an important role in many biological processes, including cellular differentiation and immune response, as well as disease development. The heterogeneity of cells in culture and in organisms poses a challenge for many experimental measurements. Traditional ensemble analysis based on averaging a large population of cells, as a result, masks the behavior of minority subpopulations and effectively blinding researchers to possibly interesting differences between cells. Single-cell analysis is an important and emerging field that gives insights into heterogeneity between cells and advanced cellular processes at high resolution, which is important for cancer research, regenerative medicine, immune system research and diagnostics, as well as for the production of therapeutics. Microfluidics has proven to be a leading tool for single cell analysis since device dimensions are on the same scale as those of cells, allowing for precise fluid and cell manipulation at high throughput. In this talk, I will present our recent efforts on developing droplet microfluidic technology for high throughput single cell isolation, manipulation, and analysis at the DNA, RNA and protein level with single-molecule sensitivity.