At the intersection of neurobiology and genome science, neurogenomics is the study of how the genome as a whole contributes to the evolution, development, structure, function and disease of the nervous system. While functional genomics investigates the sequence and structure of genomes as well as their ouputs in terms of transcriptomes and proteomes, neurogenomics tackles the special challenges of studying the nervous system. This is an highly complex tissue composed by hundreds of different cell types that are organized in circuits and present specific function. By the integration of knowledge on the anatomical and physiological organization of neural networks with gene expression data of specific populations of neurons, unexpected cellular functions, metabolic pathways and regulatory networks may be unveiled while new electrophysiological experiments can be designed. Neurogenomics can also provide new cues on the understanding of neurodegenerative diseases by identifying common molecular pathways in neurodegeneration and cell type-specific gene expression patterns that may underscore selective susceptibility of specific neurons in disease. Neurogenomics is presently at a very exciting crossroad since recent discoveries have challenged the classic model of gene organization and information flow providing potential new regulatory layers of neuronal cell function: among them, the identification of long non-coding RNAs and the description of somatic neuronal genome variants due to retrotransposition.