In Biology, many tools exist to study individual cells in culture but there is a paucity of tools to study the microenvironment in which cells live and grow in vivo. The microenvironment is the complex milieu of chemical and physical signaling that enables cells to form and function as organisms. Signaling between cells and extracellular structures is critical to normal growth and wound healing as well as malignant transitions and cancer growth. We have been exploring the use of magnetic nanoparticles to explore the microenvironment in vivo. It is not yet possible to image structures at microscopic scales in vivo as AFM does in vitro or as MRI does at macroscopic scales in vivo, but we can study some key features of the microenvironment using the Brownian motion of magnetic nanoparticles. We can observe the periodic motion of magnetic nanoparticles at very low levels and we are using those measurements to glean information about the microenvironment that includes: temperature, viscosity, chemical binding, and physical stiffness. Most of the applications discussed will be in the study of cancer targeted to both diagnostic and therapeutic patient care as well as in basic understanding of malignancy.