Improvements in diagnostic measures for biomedical applications have been investigated in various studies for better interpretations of biological abnormalities and several medical conditions. The use of imaging techniques, such as magnetic resonance imaging (MRI), is widespread and becoming a standard procedure for such specialized applications. A major avenue being studied in MRI is the use of magnetic nanoparticles (NPs) as contrast agents (CAs). Among various approaches, current research also incorporates use of superparamagnetic iron oxide NPs and manganese-based NPs with biocompatible coatings for improved stability and reduced biodegradation when exposed to a biological environment. In this review, recent advances with these types of magnetic NPs and their potential use as CAs in MRI are reported, as well as new insights into the selectivity and cellular transport mechanism that occurs following injection.