Visualization of deep biological structures in human and animal bodies is not possible through the naked eye due to the scattering of visible light by tissues in tolerable intensities. Different types of imaging modalities based on electromagnetic and pressure waves have been developed that help us image deep biological tissues with varying resolution and contrast. Some of the most widely used modalities are X-ray imaging, ultrasound imaging, MRI imaging, fluorescence imaging, and photoacoustic imaging. Although these techniques have significantly helped the advancement of our understanding of deep biological tissues and functions, they often require the use of exogenous contrast agents to improve their image quality for better investigation. Nanoparticle-based contrast agents have captivated scientists because of multiple advantages associated with them such as their excellent photophysical and chemical properties, ability to be precisely delivered at the target, and superlative tunability. This article is aimed to give a brief outlook on the recent state of art advances in the usage of nanoparticles for preclinical and clinical bioimaging through fluorescence, photoacoustic, and MRI imaging modalities.