In this review, we are going to demonstrate the recent progresses in inorganic nanomaterial-based nanomedicines and their labeling for effective biological imaging. Nanomaterials which are classified according to their dimensionality, from zero- to three-dimensions can be utilized as nanomedicines including drug delivery, therapy and diagnosis. In the following section, the labeling of nanomaterials with various contrasting agents are introduced. Various labeling agents like fluorescence, quantum dots, upconversion nanoparticles, magnetic particles and radioisotopes can be tagged on nanomaterials for effective imaging such as optical, magnetic resonance, computed tomography, positron emission tomography and etc. The labeling of contrasting agent on nanomedicine can be summarized into intercalation, surface modification, embedment and combination depending on how and where the label is tagged. Through these approaches, multimodal biological imaging and multifunctional nanomedicine could be suggested.