Several isoforms of estrogen receptor (ER, NR3A2) have been reported, including variants with different N terminal ends. In rodents, two in frame ATGs are used to produce proteins of 530 and 549 amino acids, respectively. In humans, the upstream ATG is out of frame in all clones reported, until recently, when human clones with an extra A-T bp placing the upstream ATG in frame were reported. The authors suggested that this could represent a novel polymorphism in the ER gene. Since human ER548 (hER548) and hER530 display different functional characteristics in vitro, it is of interest to determine if this variant constitutes a polymorphism in human populations. We therefore determined the frequency of this novel isoform in several populations including African (n = 96), Caucasian (n = 100) and Asian (n = 128) subjects using Denaturing High-Performance Liquid Chromatography (DHPLC). We did not detect any alleles that correspond to hER548 in these samples or in additional samples of heterogeneous origin. It is concluded that hER548 is not a common variant in Africans, Caucasians or Asians.