Molecular imaging fundamentally changes the way we look at cancer. Imaging paradigms are now shifting away from classical morphological measures towards the assessment of functional, metabolic, cellular, and molecular information in vivo. Interdisciplinary driven developments of imaging methodology and probe molecules utilizing animal models of human cancers have enhanced our ability to non-invasively characterize neoplastic tissue and follow anti-cancer treatments. Preclinical molecular imaging offers a whole palette of excellent methodology to choose from. We will focus on positron emission tomography (PET) and magnetic resonance imaging (MRI) techniques, since they provide excellent and complementary molecular imaging capabilities and bear high potential for clinical translation. Prerequisites and consequences of using animal models as surrogates of human cancers in preclinical molecular imaging are outlined. We present physical principles, values and limitations of PET and MRI as molecular imaging modalities and comment on their high potential to non-invasively assess information on hypoxia, angiogenesis, apoptosis, gene expression, metabolism, and cell trafficking in preclinical cancer research.