Previous studies from our laboratory have shown that spontaneously hypertensive rats have increased atrial natriuretic peptide stores and reduced norepinephrine release from nerve terminals in the anterior hypothalamus. We have postulated that atrial natriuretic peptide inhibits norepinephrine release in anterior hypothalamus, reducing excitation of sympathoinhibitory neurons, increasing sympathetic outflow, and elevating blood pressure in this model. The current study tested the hypothesis that atrial natriuretic peptide messenger RNA (mRNA) transcript levels are increased in anterior hypothalamus of spontaneously hypertensive rats compared with normotensive Wistar-Kyoto rats. Atrial natriuretic peptide mRNA in hypothalamic regions was measured by the quantitative polymerase chain reaction technique using a p-SELECT mutant atrial natriuretic peptide RNA as an internal standard. Atrial natriuretic peptide mRNA from hypothalamic regions of spontaneously hypertensive and Wistar-Kyoto rats and the internal standard were coamplified in a single reaction in which the same primers were used. Since the polymerase chain reaction product of the internal standard contained a new EcoRI restriction site, it could be distinguished from the atrial natriuretic peptide mRNA product by EcoRI digestion after the polymerase chain reaction. We found regional inhomogeneity of atrial natriuretic peptide mRNA in the hypothalamus of spontaneously hypertensive and Wistar-Kyoto rats, but we found no significant differences in atrial natriuretic peptide mRNA levels in anterior, posterior, or ventral hypothalamic areas between spontaneously hypertensive rats and Wistar-Kyoto rats fed normal (1%) or high (8%) salt diets. These data do not support the hypothesis that increased atrial natriuretic peptide stores in anterior hypothalamus of spontaneously hypertensive rats are related to increased gene transcription.