The immune system is composed of a variety of cells that act in a coordinated fashion in order to protect the organism against a multitude of different pathogens. The great variability of existing pathogens corresponds to a similar high heterogeneity of the immune cells. The study of a single immune cell, the fundamental unit of immunity, has recently transformed from a qualitative microscopic imaging to a nearly complete quantitative transcriptomic analysis. This shift has been driven by the rapid development of multiple single-cell technologies. These new advances are expected to boost the detection of less frequent cell types and transient or intermediate cell states. They will highlight the individuality of each single cell and greatly expand the resolution of current available classifications and differentiation trajectory. In this review we discussed the recent advancement and application of single cell technologies, their limitations and future applications to study the immune system. This article is protected by copyright. All rights reserved.