Microfluidic fraction collectors fractionating a sample stream into discrete sample volumes are provided. Fluid flow control mechanisms (22, 24, 26, 112, 114, 116, 492, 716A-716E) divert selected portions of a sample stream from an inlet channel (707) into one or more branch channels (708-712). The fluid flow control mechanisms may be passive, relying on sample volume and fluidic impedance to establish the sample collection sequence. Alternatively, active fluid flow control mechanisms may be controlled, with or without feedback, to establish the sample collection sequence.