The sense of smell relies on the monoallelic and monogenic expression of odorant receptor (OR) genes. Noncoding RNAs (RNAs that are not translated into proteins) may potentially be involved in the regulation of OR gene expression, but their roles in olfactory tissues remain elusive. Here we describe a protocol for isolating nuclear and cytoplasmic RNA fractions from mouse olfactory epithelium. The dissected tissue is subjected to cellular fractionation and RNA is extracted from the nuclear and cytoplasmic fractions. The purified RNA is then subjected to RT-PCR analysis, to verify the enrichment of nuclear/cytoplasm transcripts and control the quality of the fractionation. Determination of the subcellular localization of different RNAs may contribute to the identification of RNAs with regulatory functions in olfaction.