Magnetomotive optical coherence tomography (MM-OCT) is an important tool for the visualization and quantitative assessment of magnetic nanoparticles in tissues. In this study, we demonstrate the use of MM-OCT for quantitative measurement of magnetic iron oxide nanoparticle transport and concentration in ex vivo muscle, lung, and liver tissues. The effect of temperature on the dynamics of these nanoparticles is also analyzed. We observe that the rate of transport of nanoparticles in tissues is directly related to the elasticity of tissues, and describe how the origin of the MM-OCT signal is associated with nanoparticle binding. These results improve our understanding of how iron oxide nanoparticles behave dynamically in biological tissues, which has direct implications for medical and biological applications of targeted nanoparticles for contrast enhancement and therapy. © 2006 IEEE.