Abstract: Disclosed is a membrane filter system comprising an integral plastic holder (1, 23) having a filter receiving section (2, 24) for receiving a membrane filter (3, 30) that collects target microorganism contained in sample solution, a funnel mount (9, 25) positioned at a level higher than the filter receiving section for carrying thereon a cup-shaped paper funnel (12, 33) adapted to receive the sample solution, and a drainage (7, 28) communicated with the filter receiving section. The funnel has a bottom sheet or a paper filter (14, 35) and a bottom peripheral flange (15, 36) surrounding the bottom sheet. Resin seal means (11, 22) is fitted to the funnel mount to provide liquid-tight engagement between the funnel and the holder. The bottom sheet of the funnel is positioned above the membrane filter and serves as a primary filter for collecting particles in the sample solution larger than the target microorganism before the sample solution reaches the membrane filter.