Background: The estrogen-related receptor a (ERRa or NR3B1) is a transcription factor from the nuclear receptor super-family, group III. The gene encoding ERRa (ESRRA) is located on chromosome 11q13, a region showing genetic linkage to body mass index and fat percentage. Through interaction with the peroxisome proliferator-activated receptor-g coactivator-1a (PGC-1a), ERRa regulates key enzymes involved in the b-oxidation of fatty acids. Results: By screening 48 overweight or obese subjects for variants in the exons, exon-intron boundaries and 1000 base pairs (bp) of the promoter region of ESRRA using bi-directional nucleotide sequencing, we identified seven variants. Four rare variants had minor allele frequencies (MAF) below 1%: Pro369Pro, Gly406Asp, 3 0 UTR þ 418G4A, 3 0 UTR þ 505C4A. Two singlenucleotide polymorphisms, Pro116Pro and IVS6 þ 65C4T (MAF 15%), were in complete linkage disequilibrium (LD) (r 2 ¼ 1). We also confirmed the presence of a reported 23 bp microsatellite repeat (ESRRA23). The Pro116Pro and ESRRA23 variants were not associated with obesity, type 2 diabetes or related phenotypes in a large population-based study of 6365 Danish whites. The two variants were examined for interactions with variants in the peroxisome proliferator-activated receptor-g coactivator-1a and -b; however, no evidence of epistatic effects between the variants was demonstrated. Conclusion: The ESRRA23 and Pro116Pro variants of the gene encoding ERRa are not associated with obesity, type 2 diabetes or related quantitative traits in the examined Danish whites.