Nucleated cells in blood like white blood cells (WBCs) and other rare cells including peripheral blood stem cells (PBSCs) and circulating tumor cells (CTCs) possess significant value for patient monitoring and clinical diagnosis. Enrichment of nucleated cells from contaminating red blood cells (RBCs) using label-free techniques without the use of antibodies or centrifugation is highly desirable to ensure minimal cell loss and activation. To accomplish this, we demonstrate proof-of-concept of a new microfluidic technique that combines aqueous phase partitioning with inertial focusing to accomplish enrichment of nucleated cells in blood. This technique exploits selective affinity of RBCs to the dextran phase (DEX) to accomplish initial separation which is amplified by inertial forces that develop in high-aspect-ratio channels. In our experiments, we spiked RBC samples with representative nucleated cells, MOLT-3 cells (human, peripheral blood, T lymphoblast cell line) and MCF-7 cells (human breast cancer cell line) in a ratio of 500 : 1 (RBCs : nucleated cells) and accomplished depletion of ∼96% of RBCs while retaining ∼98% of nucleated cells. Higher purity can be accomplished by subjecting the enriched nucleated cell mixture to a second pass via the same process. The second pass further enhances RBC depletion (>99% of initial concentration) whereas nucleated cells were recovered without any further loss. This technique therefore has the potential to be utilized either alone or as a sample preparation tool in the clinical and research setting for various clinical and research applications. © 2013 The Royal Society of Chemistry.