Using reverse phase high performance liquid chromatography (RP-HPLC) coupled with two radioimmunoassays for atrial natriuretic polypeptide (ANP) with different specificities, we investigated the nature of .alpha.-rat ANP-like immunoreactivity (.alpha.-rANP-LI) with a low molecular weight in the rat brain. Two major peaks with .alpha.-rANP-LI in the extract from rat whole brains were eluted in the vicinity of the elution position of synthetic .alpha.-rANP, a 28-amino acid polypeptide. These two components co-migrated with synthetic .alpha.-rANP (4-28) and .alpha.-rANP (5-28), respectively. The peak corresponding to .alpha.-rANP (4-28) was the highest, and only a little .alpha.-rANP-LI was detected at the elution position of .alpha.-rANP. An identical profile in RP-HPLC was also observed in the extract from the rat hypothalamus. These results indicate that the major components of .alpha.-rANP-LI with a low molecular weight in the rat brain are .alpha.-rAMP (4-28) and .alpha.-rANP (5-28).