The melanocortin-3 receptor is a vital link in the leptin-melanocortin signaling pathway in the brain and has a role in the regulation of energy homeostasis. It was hypothesized that common polymorphisms in MC3R could increase susceptibility for the development of obesity, but different studies have led to contradictory results. In this study, we investigated the association of SNPs in MC3R with the development of obesity in an extensive Caucasian population. Using the HapMap, we selected two tagSNPs (rs6127698 and rs3746619) that cover all of the common genetic variation in MC3R and genotyped them in 1008 obese cases and 313 normal weight controls. Statistical analysis of the data showed that none of the analyzed SNPs were associated with obesity. However, linear regression analysis did show that SNP rs3746619 has an influence on weight (P=0.015) in the obese population only. Furthermore, a trend for association with BMI in the obese population was observed for this SNP (P=0.039). Taken together, these data are consistent with the involvement of rs3746619 in weight regulation among obese individuals. However, further research including replication of our results is necessary to elucidate the role of MC3R in complex obesity.