Neuroimaging is a potentially valuable tool to link individual differences in the human genome to structure and functional variations, narrowing the gaps in the casual chain from a given genetic variation to a brain disorder. Because genes are not usually expressed at the level of mental behavior, but are mediated by their molecular and cellular effects, molecular imaging could play a key role. This article reviews the literature using molecular imaging as an intermediate phenotype and/or biomarker for illness related to certain genetic alterations, focusing on the most common neurodegenerative disorders, Alzheimer’s disease (AD) and Parkinson disease.