Nanoparticles (NPs) are being implemented in a wide range of applications, and it is critical to proactively investigate their toxicity. Due to the extensive range of NPs being produced, in vitro studies are a valuable approach for toxicity screening. Key information required to support in vitro toxicity assessments include NP stability in biologically relevant media and fate once exposed to cells. Hyperspectral microscopy is a sensitive, real-time technique that combines the use of microscopy and spectroscopy for the measurement of the reflectance spectrum at individual pixels in a micrograph. This method has been used extensively for molecular imaging with plasmonic NPs as contrast agents (Aaron et al., Opt Express 16:2153−2167, 2008; Kumar et al., Nano Lett 7:1338−1343, 2007; Wax and Sokolov, Laser Photon Rev 3:146−158, 2009; Curry et al., Opt Express 14:6535–6542, 2006; Curry et al., J Biomed Opt 13:014022, 2008; Cognet et al., Proc Natl Acad Sci U S A 100:11350–11355, 2003; Sokolov et al., Cancer Res 63:1999–2004, 2003; S�nnichsen et al., Nat Biotechnol 23:741−745, 2005; Nusz et al., Anal Chem 80:984–989, 2008) and/or sensors (Nusz et al., Anal Chem 80:984–989, 2008; Ungureanu et al., Sens Actuators B 150:529−536, 2010; McFarland and Van Duyne, Nano Lett 3:1057−1062, 2003; Galush et al., Nano Lett 9:2077−2082, 2009; El-Sayed et al., Nano Lett 5:829–834, 2005). Here we describe an approach for using hyperspectral microscopy to characterize the agglomeration and stability of plasmonic NPs in biological media and their interactions with cells.