The trigeminal ganglia (TG) subserving the head and the dorsal root ganglia (DRG) subserving the rest of the body are homologous handling sensory neurons. Differences exist, as a number of signaling substances cause headache but no pain in the rest of the body. To date, very few genes involved in this difference have been identified. We aim to reveal basal gene expression levels in TG and DRG and detect genes that are differentially expressed (DE) between TG and DRG. RNA-Sequencing from six naïve rats describes the whole transcriptome expression profiles of TG and DRG. Differential expression analysis was followed by pathway analysis to identify DE processes between TG and DRG. In total, 64 genes had higher and 55 genes had lower expressed levels in TG than DRG. Higher expressed genes, including S1pr5 and Gjc2, have been related to phospholipase activity. The lower expressed genes, including several Hox genes and Slc5a7, have been related to tyrosine and phenylalanine metabolism. Tissue-specific expression was identified for Gabra6 and Gabrd in TG, and for several Hox genes in DRG. Furthermore, genes that were known to be associated with headache/migraine were mostly moderately to highly expressed in one or both tissues. We present a comprehensive overview of the expression profiles of whole tissue comparison of TG and DRG. Further, we showed DE genes/pathways between TG and DRG, including several known migraine-associated genes. This study provides a basis for further pain-related studies using TG and DRG in rats.