A method for isolation of particles of at least one given type from a sample by means of a microfluidic system; the method comprising: a step of introduction of said sample into the system through a first inlet of the system itself; a separation step, during which at least part of the particles of the given type are transferred from a main chamber to a recovery chamber of a separation unit of the system in a selective way with respect to further particles of said sample; a first outlet and a second outlet being connected to the main chamber and to the recovery chamber, respectively; the separation unit further comprising a channel, which connects the main chamber and the recovery chamber; a first feeding step, which precedes the separation step and during which at least part of said sample is fed into the main chamber; a second feeding step, which precedes the separation step and during which carrier liquid is fed into the recovery chamber; and a recovery step, which is subsequent to the separation step and during which the carrier liquid together with at least part of the particles of the given type flow out of the recovery chamber through the second outlet; the method being characterized in that the system comprises: a first valve, which is set upstream of the main chamber between the first inlet and the main chamber; a second valve, set downstream of the main chamber between the main chamber and the first outlet; a third valve, set upstream of the recovery chamber and connected to the recovery chamber; and a fourth valve, set downstream of the recovery chamber between the recovery chamber and the second outlet; the first and second valves (9, 10) being designed to regulate inflow of said sample to the main chamber; the third and fourth valves (11; 12) being designed to regulate inflow of a carrier liquid to the recovery chamber and outflow of the carrier liquid together with the particles of the given type from the recovery chamber through the second outlet; during the separation step the first, second, third, and fourth valves (9, 10, 11, 12) are closed so as to isolate the main chamber and the recovery chamber with respect to the outside. a step of introduction of said sample into the system through a first inlet of the system itself; a separation step, during which at least part of the particles of the given type are transferred from a main chamber to a recovery chamber of a separation unit of the system in a selective way with respect to further particles of said sample; a first outlet and a second outlet being connected to the main chamber and to the recovery chamber, respectively; the separation unit further comprising a channel, which connects the main chamber and the recovery chamber; a first feeding step, which precedes the separation step and during which at least part of said sample is fed into the main chamber; a second feeding step, which precedes the separation step and during which carrier liquid is fed into the recovery chamber; and a recovery step, which is subsequent to the separation step and during which the carrier liquid together with at least part of the particles of the given type flow out of the recovery chamber through the second outlet; the method being characterized in that the system comprises: a first valve, which is set upstream of the main chamber between the first inlet and the main chamber; a second valve, set downstream of the main chamber between the main chamber and the first outlet; a third valve, set upstream of the recovery chamber and connected to the recovery chamber; and a fourth valve, set downstream of the recovery chamber between the recovery chamber and the second outlet; the first and second valves (9, 10) being designed to regulate inflow of said sample to the main chamber; the third and fourth valves (11; 12) being designed to regulate inflow of a carrier liquid to the recovery chamber and outflow of the carrier liquid together with the particles of the given type from the recovery chamber through the second outlet; during the separation step the first, second, third, and fourth valves (9, 10, 11, 12) are closed so as to isolate the main chamber and the recovery chamber with respect to the outside.