Magnetic resonance imaging (MRI), one of the most powerful imaging modalities available for clinical diagnosis, has contributed significantly to phenotyping of transgenic organisms and to cellular imaging and is now gaining importance in the field of molecular imaging. Its advantage is the ability to provide in vivo information with high resolution and good soft tissue contrast as compared to established other molecular imaging methods. MRI can non-invasively report on cell localisation and migration with detailed anatomical background information, which is of great interest in cellular therapies. Recent technological advances and contrast generation strategies aim to bring MRI beyond cellular imaging to the detection of functional changes in vivo. MR based monitoring of molecular processes, requires the development of contrast agents and targeting methods as well as improvements in the methods sensitivity. Here, an overview is provided on advanced MR technologies and contrast generation strategies for this purpose. This includes MRI and MR spectroscopic methods for molecular imaging and various approaches for targeted and responsive contrast generation to visualize functional changes of particular cells. A description of different methods is provided, as well as the potentials and challenges of MR techniques for the visualization of molecular processes in vivo.