A bone collection system includes a plunger, a tube, and a manifold. The plunger has a bore therethrough, an insertion portion, and an inlet that accepts material being harvested from a patient. The insertion portion includes a filter to prevent passage of bone fragments. The tube accepts the insertion portion, defining a first and a second chamber of the tube. The filter separates the first and second chambers of the tube. The manifold is accepted by the tube, and has an outlet accepted by a suction source. The inlet of the plunger is in fluid communication with the first chamber, the first and second chambers are in fluid communication through the filter, and the second chamber is in fluid communication with the outlet. Material being harvested is drawn through the bone collection system, and bone fragments of the desired size collected in the first chamber.