Advancements in single-cell sequencing have revolutionized our understanding of complex biological systems such as the immune system and allowed us to overcome limitations in various disciplines of life science research such as oncology, developmental biology, or neurobiology (Perkel, Nature 595. https://www.nature.com/articles/d41586-021-01994-w , 2021).The BD Rhapsody™ Single-Cell Analysis System enables us to capture multimodal information from thousands of single cells in parallel ("Multiomics") covering mRNA expression levels, protein expression levels, the immune repertoire for T-cell receptors (TCR) and B-cell receptors (BCR), and the identification of antigen-specific T cells and B cells using dCODE Dextramer® (RiO) from Immudex. The system utilizes microwell-based cartridges that allow to capture a broad range of single cells and an imaging device for sample quality control and workflow quality control (including viability and multiplets). The power of Multiomics relies on simultaneously measuring several aspects of single cells, including gene expression and protein abundance, using next generation sequencing (NGS) as a single readout.Here we describe the complete BD Rhapsody™ Single-Cell Analysis System from the sample preparation including different options for the antibody and/or dCODE Dextramer® staining through to the data analysis.For updated protocols, guides, and technical bulletins, please visit the BD Scomix page: https://scomix.bd.com/hc/en-us or the BDB webpage: https://www.bdbiosciences.com/en-eu . Keywords: BD Biosciences; BD Rhapsody™ Single-Cell Analysis System; BD® AbSeq; Microwells; Multimodal Single-Cell Sequencing; Single-Cell Multiomics.