Variations of the small heterodimer partner (SHP, NR0B2) gene, an atypical nuclear receptor that inhibits transactivation by hepatocyte nuclear factor (HNF)‐4α, are associated with obesity among Japanese. The purpose of the study was to evaluate the prevalence of SHP variants among obese Danish men. Using combined SSCP and heteroduplex analysis, we analyzed the entire coding region of SHP for variants in a cohort of 750 Danish men with early‐onset obesity and genotyped a cohort of 795 nonobese control subjects using PCR‐RFLP. Functional analyses of the identified coding region variants were performed in both MIN6‐m9 and HepG2 cell lines. A total of five novel variants, including three missense variants (c.100C>G [p.R34G], c.278G>A [p.G93D], and c.415C>A [p.P139H]) and two silent variants (c.65C>T [p.Y22Y] and c.339G>A [p.P113P]) were identified. Moreover, the previously reported c.512G>C [p.G171A] polymorphism was identified. The 171A allele was not associated with obesity (p = 0.07). The 34G, 93D, and 139H‐alleles were rare variants, which were found only among obese subjects. Among the four coding region variants, the 93D‐allele showed a reduced in vitro inhibition of the HNF‐4α transactivation of the HNF‐1α promoter expression when expressed in MIN6‐m9 and HepG2 cell lines (p<0.01). In contrast to reported findings among obese Japanese, functional variants are rare among Danish men. A functional 93D variant of SHP was identified in 1 out of 750 obese and in none of 795 nonobese control subjects. Further large‐scale population studies are necessary to assess the clinical impact of this rare variant on obesity risk among European subjects. Hum Mutat 24:381–387, 2004. © 2004 Wiley‐Liss, Inc.