A biopsy device includes a tissue sample holder and a cutter defining a cutter lumen. In one example, the tissue sample holder has a manifold, a plurality of chambers that are configured to separately hold tissue samples, and a cup configured to cover the manifold and chambers. The tissue sample holder is rotatable to successively align the chambers with the cutter lumen. A longitudinal passage extends along the manifold, and is positioned between two of the chambers. The manifold may be rotated to align the passage with the cutter lumen and with an opening in the cup. The passage of the manifold and the opening in the cup are configured to permit a portion of an instrument to be inserted through the opening and passage and into the cutter lumen. The instrument may be used to introduce one or more markers or medicine, etc., to a biopsy site.