Occlusion is the major limitation of plastic biliary endoprostheses (PBE), making regular stent exchange necessary. The aim of the in vitro analysis was to evaluate the cleansing effect of shockwave application (SWA) on occluded PBE. Thirty-five PBE removed from 24 patients were analyzed. Three hundred and fifty shockwave pulses were administered every 10 mm along the prosthesis stored in a liquid-filled latex balloon. Occlusion rates were measured before and after SWA. The cleansing rate was calculated in comparison to the native prosthesis. Mean occlusion rate was 76 ± 30% (Range 16–100%) before SWA. Cleansing effect was 47 ± 52% (0–100%) after SWA. Cleaning was complete (100%) in seven (20%) and satisfying (75–99%) in another seven prostheses. Degree of stent occlusion and indwelling time were significantly associated to the cleansing effect. In conclusion, SWA showed a limited cleaning effect in clogged PBE and is no suitable alternative for regular stent replacement to date.