Biologic scaffolds composed of extracellular matrix (ECM) are widely used in both preclinical animal studies and in many clinical applications to repair and reconstruct tissues. Recently, 3-dimensional ECM constructs have been investigated for use in whole organ engineering applications. ECM scaffolds are prepared by decellularization of mammalian tissues and the ECM provides natural biologic cues that facilitate the restoration of site appropriate and functional tissue. Preservation of the native ECM constituents (i.e., three-dimensional ultrastructure and biochemical composition) during the decellularization process would theoretically result in the ideal scaffold for tissue remodeling. However, all methods of decellularization invariably disrupt the ECM to some degree. Decellularization of tissues and organs for the production of ECM bioscaffolds requires a balance between maintaining native ECM structure and the removal of cellular materials such as DNA, mitochondria, membrane lipids, and cytosolic proteins. These remnant cellular components can elicit an adverse inflammatory response and inhibit constructive remodeling if not adequately removed. Many variables including cell density, matrix density, thickness, and morphology can affect the extent of tissue and organ decellularization and thus the integrity and physical properties of the resulting ECM scaffold. This review describes currently used decellularization techniques, and the effects of these techniques upon the host response to the material.