A possible link between fibromyalgia (FM) and obesity has been recently suggested but very scanty data on the prevalence of FM in obese populations are available. The aims of the present cross-sectional study were: 1) to estimate the prevalence of FM in a population of obese patients undergoing rehabilitation and 2) to investigate the effect of FM on obese patients' functional capacities. One hundred and thirty Italian obese (Body Mass Index, BMI ≥ 30) patients admitted to hospital for 1-month rehabilitation treatment took part in the study. All participants were interviewed by a rheumatologist according to the 2010 American College of Rheumatology (ACR) diagnostic criteria for FM. At admission and discharge from hospital (on average, after 28 days), the following measures were compared between the group of patients with FM and the other patients: body weight, body mass index, functional independence (FIM), obesity-related disability (TSD-OC), self-reported functioning and the Timed-Up-Go (TUG) test. Thirty seven patients out of 130 fulfilled the diagnostic criteria for FM. The prevalence rate was 27.7% (95% CI: 20 to 35.4). Between-group comparisons showed that FM patients had higher disability level at the first assessment, had lower scores on the FIM at the final assessment, scored lower on self-reported functioning both at the first and the final assessments and had a lower body weight. The prevalence of FM in our study is much higher than the rates reported in the general normal-weight population (on average, 3.5%) and the 5.15% rate previously reported in a bariatric population. Functional data showed that the FM obese group yielded lower performance capacity and higher disability level as compared to the non-FM obese group. However, due to the relatively small sample size and the selected population, such results need to be confirmed in larger obese subpopulations.