We present a low-cost, flow-through nanocytometer that utilizes a colloidal suspension of non-functionalized magnetic nanoparticles for label-free manipulation and separation of microparticles. Our size-based separation is mediated by angular momentum transfer from magnetically excited ferrofluid particles to microparticles. The nanocytometer is capable of rapidly sorting and focusing two or more species, with up to 99% separation efficiency and a throughput of 3 × 10(4) particles/s per mm(2) of channel cross-section. The device is readily scalable and applicable to live cell sorting with biocompatible ferrofluids, offering competitive cytometer performance in a simple and inexpensive package.