Recent advances in the field of nanomedicine offer the promise of better diagnostic and therapeutic options. Synthetic chemists are making strides in developing nanoparticle constructs that can be used as platforms for attaching different functionalities for the purposes of molecular imaging and targeted drug delivery. As new nanoparticles are developed, it is imperative to evaluate their biological effectiveness by in vitro and in vivo screening techniques. While the in vitro results give insight into the cellular structure and function at sub-cellular level, the in vivo and ex vivo data give vital information about the pharmacokinetics of these novel particles, along with their ability to reach the desired target. This three-way information is pertinent to developing effective drugs and imaging probes for targeting key cancer/inflammation biomarkers such as the alphavbeta3 integrin. Labeling nanoparticles with positron emitting radionuclides can speed up this evaluation. In fact, small animal Positron Emission Tomography (PET) scanners allow researchers to quantitatively image the uptake of candidate nanocarriers at the target site with high sensitivity. In addition to conventional ex vivo biodistribution techniques, the pharmacokinetic profile of new nanomaterials with potential medical application can be obtained with dynamic and/or longitudinal PET studies on a relatively small number of laboratory animals. This article will focus on some of the approaches to label nanoparticles with positron emitting radionuclides along with in vitro and in vivo protocols that have been optimized and are being used for evaluating nanoparticles.