The objective of the present study is to determine whether benign joint hypermobility syndrome (BJHS) modifies the risk of mitral valve prolapse (MVP) in patients with fibromyalgia (FM). Female patients fulfilling the 1990 American College of Rheumatology (ACR) diagnostic criteria for FM were included into the study. Joint hypermobility and BJHS were assessed using Beighton's scoring system and Brighton criteria, respectively. Echocardiograpic evaluation was performed in order to test the presence of MVP. Of the 75 female FM patients, 68.0 % (n = 51) and 20.0 % (n = 15) were diagnosed with BJHS and MVP, respectively. The frequencies of both MVP and BJHS seemed higher than the general population prevalence (p = 0.000 for both). The frequency of MVP was significantly higher in patients with BJHS than that in patients without BJHS (p = 0.028). In addition, BJHS was found to increase the risk of MVP approximately ninefold [odds ratio (OR) 8.7, 95 % confidence interval (CI) 1.1-70.7]. As a result, BJHS and MVP are both common in female patients with FM. Moreover, among the female patients with FM, those with BJHS are about nine times more prone to MVP than those without BJHS. Cardiologic assessment might be added to the routine follow-up strategies in FM patients with BJHS in order to exclude the cardiac pathologies, especially MVP.