Studying biology through a high-throughput lens has enabled many advancements in academia and healthcare. Yet for cytometry, the analysis and sorting of cells, current tools necessarily face trade-offs between throughput, accuracy, and viability. Microfluidics, the highly controllable manipulation of fluids on the microscale, has potential to address these limitations. Herein, we present the development and application of an ultrahigh-throughput immunomagnetic microfluidic cytometry platform technology. The technology, termed microfluidic cell sorting (MICS), is capable of sorting 4.4x108 live cells/hour/device and contains reusable components and a user-friendly external set up to facilitate deployment to non-expert users. Device performance was validated using immortalized cell lines and was shown to be able to isolate clinically relevant quantities (108 ) of mature CD56dimCD16bright natural killer cells from primary samples in hours. To demonstrate further utility in cell biology, MICS was used to facilitate a genome-wide CRISPR screen in embryonic stem cells, a challenging cell type for sorting. This screen identified homeobox protein CDX-2 as a negative genetic regulator of mesoderm differentiation efficiency. Knock-out of CDX2 resulted in a 2-fold increase in mesoderm specification at day 6 and increased proportions of both hematopoietic stem cell and lymphocyte progenitors at later time points. Finally, MICS was used in combination with an unsupervised k-means clustering algorithm, to create a novel approach to phage display antibody discovery. This approach, termed μCellect, performs fab-antigen binding in a heterogenous mixture of antigenexpressing and background cells and chooses candidates for validation by identifying underlying motifs in primary protein structure that contribute to affinity. In a proof-of-concept screen pursuing Frizzled-7, a challenging oncology target, μCellect discovered antibodies with picomolar affinities and increased selectivity relative to first-in-class reagents in only two selection rounds. The approaches and findings presented in this work demonstrate that MICS is a high-throughput, high-precision cytometry tool with the potential to unlock new approaches to studying cell biology. In addition, the approaches used to develop the MICS technology provide novel contributions to microfluidics and adjacent research fields.