A microfluidic system (1) for the isolation of cells (C1) of at least one given type from a sample; the system (1) comprises a separation unit (3), for transferring at least part of the cells (C1) of the given type from a main chamber (4) to a recovery chamber (5) in a substantially selective way with respect to further cells (C2) of the sample; two valves (9, 10) are set upstream and downstream of the main chamber (4); two valves (11, 12) are set upstream and downstream of the recovery chamber (5); a control assembly (23) is designed to govern the aforementioned valves (9, 10, 11, 12); the system (1) proposed enables isolation of the cells with a high degree of reproducibility and precision.