A substantial part of nanomedicine focuses on drug design and employing magnetic nanomaterials with multifunctional polymers, lipids or proteins. High-throughput drug discovery requires a tool which is able to analyze, manipulate, and sort objects containing known doses of magnetic nanoparticles associated with medications. A promising route relies on the implementation of magnetically-labeled biochemical species combining magnetoresistive sensors. In-flow detection based on magnetoresistive sensors has been demonstrated recently, representing first steps towards the integration of magnetic sensor elements into fluidic channels. However, up to date, progress is restrained to the mere sensing and counting of magnetic objects. Advanced and quantitative analysis, which is the main advantage of e.g. optical flow cytometry, has not been explored so far with magnetic sensors. Apart from detection and analysis, sorting of species is invaluable in diagnostic devices. We report a magnetoresistive emulsion analyzer which is capable of detection, multiparametric analysis and sorting of ferrofluid droplets. The device offers important complementarity to conventional optical approaches involving ferrofluids, and paves the way to the development of novel compact tools for diagnostics and nanomedicine.