The compelling need for early detection and chemical characterization of protein deposits in conformational disorders has always relied on immunohistochemical techniques performed on diagnostic biopsy specimens. Although the identity of the culprit can be assessed, the molecular nature of the defect still requires the analysis of the extracted material. The purpose of this chapter is to provide investigators with a method to extract and analyze—from minute residual diagnostic tissue biopsies—the deposited proteins. If done successfully, the technique will allow further investigation by molecular studies, while the patient is still being evaluated.