Functional analysis of lymphocytes is important for development of vaccines and diagnosis/treatment of various immune-related diseases. In this review, we describe multifunctional microwell arrays that enable functional analysis of lymphocytes at the single cell level. We first discuss key parameters for microwell array design. Then, we describe how different types of multifunctional microwell arrays were developed for various applications, including live cell imaging of lymphocyte activation, proliferation, and differentiation, and analyses of effector functions such as cytokine secretion and target cell lysis. Incorporation of novel surface chemistries and functional materials into microwell arrays for enhancing sensing capabilities will widen applications of this technology. Multifunctional microwell arrays will be a powerful tool for the development of novel therapeutics against immune-related diseases, in particular, for cancer immunotherapy.