The Food and Drug Administration (FDA) and pharmaceutical industry have used standards to assess material biocompatibility, immunotoxicity, purity, and sterility (as well as many other properties) for several decades. Nanoparticle developers and manufacturers leverage well-established methods as much as possible. However, the unique properties of nanomaterials often interfere with standardized protocols, giving false-positive or false-negative results. This chapter provides details of some of the problems which can arise during the characterization of nanoparticle samples. Additionally, we discuss ways to identify, avoid, and resolve such interference, with emphasis on the use of inhibition and enhancement controls.