Peptide major histocompatibility complex (pMHC) multimers have been used since decades to identify, isolate and analyze antigen-specific T cells by flow (and more recently mass) cytometry. Yet well established as a standard technology, improvements are still required to face the growing needs of personalized immune monitoring. Here we review the latest developments about (i) the quality of pMHC class I and II monomers, (ii) the importance of the multimeric scaffold, (iii) the staining conditions and (iv) the high-throughput synthesis of pMHC monomers. Finally, innovative multiplexed, combinatorial strategies for parallel detection of antigen-specific T cells in a single sample are discussed.