The estrogen receptor (ER) ligand binding domain (LBD; D, E and F domains) of the green anole, Anolis carolinensis, was cloned using degenerate PCR primers coupled with the 3' RACE (rapid amplification of cDNA ends) strategy. Two forward degenerate PCR primers complementary to the DNA binding domain (C domain) and a reverse degenerate PCR primer complementary to a highly conserved region of the E domain were derived from a consensus sequence generated from a multiple species sequence alignment of 10 known ER sequences. Using successive rounds of PCR, an 800 bp fragment representing approximately 75% of the region of interest was amplified and sequenced. Based on this sequence, green anole ER specific primers were generated and used in conjunction with the oligo dT primer to clone the remaining 3' end of the cDNA. The ER LBD amino acid sequence of the anole exhibits a high degree of sequence identity (79%) and similarity (83%) when compared to the human ER as determined from sequence comparisons using the GCG suite of programs. The boundaries of the individual D, E and F domains for the green anole ER were determined from a primary sequence alignment to the human ER LBD. The E domain displayed the highest degree of sequence identity (89%) when compared to the human ER, followed by the D (57%) and F (32%) domains. Relative to other species, the green anole ER LBD was intermediate in terms of its sequence identity when compared to the human mouse (90%), chicken (82%), Xenopus (70%) and rainbow trout (40%) ER LBDs. This is the first complete reptilian ER LBD sequence reported and will be used to prepare recombinant chimeric anole ER LBD proteins to identify and assess chemicals and complex mixtures for estrogenic activity that may be specific to reptilian species.