A method of analyzing at least one tissue sample which has been removed from a patient using a biopsy system, the method comprising: (a) depositing the at least one tissue sample into a removable sample tray by transporting the at least one tissue sample through a hollow cutter of the biopsy system and into the removable sample tray; (b) removing the at least one tissue sample from the biopsy system, the act of removing the at least one tissue sample from the biopsy system including removing the removable sample tray away from the biopsy system; (c) storing information relating to the at least tissue sample in a tracking system; (d) forming, on a tissue container, a first tag associated with the at least one tissue sample, the first tag including the information relating to the at least one tissue sample stored in the tracking system; (e) forming, on a transport container, a second tag including the information contained in the first tag and associated with the at least one tissue sample; (f) placing the removable sample tray containing the at least one tissue sample into the tissue container; (g) placing the tissue container and the removable sample tray containing the at least one tissue sample into the transport container at a first location associated with removal of the at least one tissue sample; (h) scanning the first and second tag from the tissue container and the transport container at the first location with an electronic scanning system of the tracking system to ensure that the first and second tag are both associated with the at least one tissue sample; (i) transporting the transport container containing the tissue container to a secondary location after scanning of the first tag and the second tag; (j) scanning the first tag to confirm, with the tracking system, correspondence between the first tag and the second tag after scanning the second tag upon arrival to the secondary location. (a) depositing the at least one tissue sample into a removable sample tray by transporting the at least one tissue sample through a hollow cutter of the biopsy system and into the removable sample tray; (b) removing the at least one tissue sample from the biopsy system, the act of removing the at least one tissue sample from the biopsy system including removing the removable sample tray away from the biopsy system; (c) storing information relating to the at least tissue sample in a tracking system; (d) forming, on a tissue container, a first tag associated with the at least one tissue sample, the first tag including the information relating to the at least one tissue sample stored in the tracking system; (e) forming, on a transport container, a second tag including the information contained in the first tag and associated with the at least one tissue sample; (f) placing the removable sample tray containing the at least one tissue sample into the tissue container; (g) placing the tissue container and the removable sample tray containing the at least one tissue sample into the transport container at a first location associated with removal of the at least one tissue sample; (h) scanning the first and second tag from the tissue container and the transport container at the first location with an electronic scanning system of the tracking system to ensure that the first and second tag are both associated with the at least one tissue sample; (i) transporting the transport container containing the tissue container to a secondary location after scanning of the first tag and the second tag; (j) scanning the first tag to confirm, with the tracking system, correspondence between the first tag and the second tag after scanning the second tag upon arrival to the secondary location.