Guggulsterone 1, the active principle of guggulipid, has been used in ethnic medicine for thousands of years for its antinflammatory and antilipidemic activities. The activities of 1 are apparently mediated by its interaction with an array of nuclear receptors, including endocrine steroid receptors and metabolic lipid receptors. Although relatively weak, the activity at the metabolic farnesoid X receptor (FXR) is particularly intriguing, as 1 is, so far, the only antagonist known for this receptor, with a peculiar ability of gene selective modulation. We report here a systematic study aimed at identifying the potential binding pocket of 1 at FXR. Although 1 could be docked into the canonical binding site, we identified a novel, so far undescribed binding pocket, localized near the loop region between helix 1 and helix 2. This novel binding pocket may explain some of the peculiar characteristics of 1 when acting at FXR.