Due to the rapid development of a diverse array of nanoparticles, used in a wide variety of products, there are now many international activities to assess the potential toxicity of these materials. These particles are developed due to properties such as catalytic reactivity, high surface area, light emission properties, and others. Such properties have the potential to interfere in many well-established toxicity testing protocols. This article outlines some of the most frequently used assays to assess the cytotoxity and biological reactivity of nanoparticles in vitro. The article identifies key issues that need to be addressed in relation to inclusion of relevant controls, assessing particles for their ability to interfere in the assays, and using systematic approaches to prevent misinterpretation of data. The protocols discussed range from simple cytotoxicity assays, to measurement of reactive oxygen species and oxidative stress, activation of proinflammatory signaling, and finally genotoxicity. The aim of this review is to share knowledge relating to nanoparticle toxicity testing in order to provide advice and support for guidelines, regulatory bodies, and for scientists in general.