A microfluidic device for separating target components from a source fluid includes one or more source channels connected to one or more collection channels by one or more transfer channels. The target components of the source fluid can be magnetic or bound to magnetic particles using a know binding agent. A source fluid containing magnetically bound target components can be pumped through the source channel of the microfluidic device. A magnetic field gradient can be applied to the source fluid in the source channel causing the magnetically bound target components to migrate through the transfer channel into the collection channel. The collection channel can include a collection fluid that is stagnant until a predefined volume of source fluid is processed or a predefined volume of target components accumulate in the collection channel, at which point collection fluid can be pumped into the collection channel to flush the target components out of the collection channel. The target components can be subsequently analyzed for detection and diagnosis.