Over 200 murine imprinted genes have currently been identified, many are expressed in the brain, and a subset have been associated with neurological and behavioural phenotypes. These studies have led to the suggestion that imprinted genes show enriched expression in certain key brain functions; however, this has never been formally tested. Here we use fifteen available single-cell RNA sequencing datasets to investigate imprinted gene over-representation in the brain, with the aim of identifying key hotspots of expression and, by extension, function. We establish that imprinted genes are indeed over-represented in the adult brain compared to other adult tissues, and in neurons specifically compared to other cell-types. Brain wide datasets allowed us to demonstrate enrichment of imprinted genes in the hypothalamus, ventral midbrain, pons and medulla. Finally, using scRNA-seq datasets focusing on these regions of enrichment, we were able to identify hypothalamic neuroendocrine populations and the monoaminergic hindbrain neurons as specific hotspots of imprinted gene expression. These analyses provide a robust assessment of the neural systems on which imprinted genes converge and in turn suggest the neuronal regulation of motivated behaviours such as feeding, parental behaviour and sleep as functional hotspots for imprinting.