Abstract: A vacuum system for removal of debris in the form of shavings, particles, or the like has been developed for use inside of a cryostat to evacuate and collect such material as it is generated during specimen preparation using a microtome, also inside of the cryostat. The system includes a vacuum assembly unit containing a vacuum collection nozzle having a suction duct. The cold assembly unit is moveably positioned adjacent to the microtome knife so that debris is suctioned away and removed concurrent with or immediately after its production during cryotomy, and is captured in a cold primary filter. The frozen debris does not melt, but remains rigid while it freeze-dries and is trapped on the filter as cold air flows over and through it, thereby maintaining the collected waste material in a very porous state.