A device and method for mapping, diagnosing and treating disorders or other diseases, disorders or conditions (e.g., bleeding, ischemic or necrotic tissue, and presence of certain chemicals or substances) of the intestinal tract is provided using a capsule passing through the intestinal tract and sensing optical characteristics as the capsule passes through. Further, a capsule tracking system is provided for tracking a capsules location along the length of an intestinal tract as various treatment and/or sensing modalities are employed. In one variation, an acoustic signal is used to determine the location of the capsule. A map of optical characteristics may be derived from the pass of a capsule to diagnose the disorder or disease. The capsule or subsequently passed capsules may treat, further diagnose or mark the intestinal tract at a determined location along its length.
