With many desirable properties, nanoparticles hold tremendous potential for in vivo molecular imaging and improving the efficacy of small-molecule drugs. The pharmacokinetics (PK) and tissue distribution of nanoparticles largely define their in vivo performance and potential toxicity, which are fundamental issues that need to be elucidated. In this review article, we summarized how molecular imaging techniques (e.g., positron emission tomography, fluorescence imaging, etc.) can facilitate the investigation of PK profiles of nanoparticles using carbon nanotubes (CNTs) and quantum dots (QDs) as representative examples. Different imaging techniques can provide useful insights in monitoring the in vivo behavior and tissue distribution of these nanoparticles, and a number of strategies were utilized to optimize the PK profiles of CNTs and QDs. Based on the available literature reports, it can be concluded that chemical/physical properties of the nanoparticles (e.g., surface functionalization, hydrodynamic size, shape, surface charge, etc.), along with the administration routes/doses, can play critical roles in determining the PK and biodistribution pattern of nanoparticles. Robust chemistry for surface modification of nanoparticles is a prerequisite for successful future biomedical/clinical applications.