We designed a simple and reliable procedure allowing gene expression studies by RT-PCR in native endothelial and smooth muscle cells from rat aorta and used it to analyze the distribution of a subunit isoforms of Na⁺/K⁺-ATPase within the aorta wall. We perfused aorta with a reagent for RNA isolation (TriPure), and collected three successive fractions (E1-3) and the remaining tissue (Ao[E-]). We analyzed them by RT-PCR for endothelial markers (eNOS, von Willebrand factor, preproendothelin-1), smooth muscle markers (L-type calcium channel [Cav1.2], SM22), Na⁺/K⁺-ATPase isoforms (NaKa1, NaKa2, NaKa3) and ribosomal protein L32 (loading control). Compared to intact aorta Ao[E+], endothelial markers were enriched 3–5 fold in E1-3, but almost absent in Ao[E-]. Smooth muscle markers were undetectable in E1, increased somewhat in E2-3 and were similar in Ao[E-] and Ao[E+]. NaKa2 closely followed the expression pattern of smooth muscle markers. NaKa1 and NaKa3 were uniformly expressed in all fractions. NaKa3 expression in whole blood (a likely contaminant) was over 100-fold higher than in aorta. Thus, (i) typical distribution patterns for mRNAs expressed preferentially in endothelial and smooth muscle cells can be recognized in fractions obtained by TriPure perfusion of intact rat aorta; (ii) aortic endothelium expresses only NaKa1, whereas smooth muscle expresses NaKa1 and NaKa2, but not NaKa3.