Aim: Over the past decade, our understanding of the transcriptional landscape in the brain has undergone a dogma-challenging expansion, revealing the intricate role of non-protein-coding RNAs (ncRNAs) in neural function, development, and disease. A large number of ncRNAs have been discovered and implicated in molecular regulatory processes involved in neural homeostasis and activity and seem to play crucial roles in neurodegenerative disorders and cancer. This study aims to assess the efficacy of in situ hybridization (ISH) in profiling long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in central nervous tissue samples, elucidating their expression patterns and potential as biomarkers.Methods: We employed AMPIVIEW™ RNA probes, powered by Enzo’s LoopRNA™ ISH technology, to target specific lncRNA and circRNA sequences. Samples from various brain tissues, including a murine disease model, were subjected to ISH to evaluate expression levels and spatial distribution.Results: Robust expression of the lncRNA Norad and the circRNA Circ018 was observed in rat and mouse brain tissue via chromogenic or fluorescent staining. Furthermore, altered expression patterns were detected in a mouse brain injury model, indicating potential implications for disease states.Conclusion: Our findings demonstrate the utility of AMPIVIEW™ RNA probes in detecting specific lncRNA and circRNA expression in fixed tissue sections, offering insights into normal brain function and disease pathology. ISH emerges as a valuable tool for characterizing the regulatory roles of not only mRNAs, but also ncRNAs in the central nervous system.