Introduction: Tropheryma whipplei is the causative agent of Whipple disease. T. whipplei has also been detected in asymptomatic carriers with a very different prevalence. To date, in Spain, there are no data regarding the prevalence of T. whipplei in a healthy population or in HIV-positive patients, or in chronic fatigue syndrome (CFS). Therefore, the aim of this work was to assess the prevalence of T. whipplei in stools in those populations. Methods: Stools from 21 HIV-negative subjects, 65 HIV-infected, and 12 CFS patients were analysed using real time-PCR. HIV-negative and positive subjects were divided into two groups, depending on the presence/absence of metabolic syndrome (MS). Positive samples were sequenced. Results: The prevalence of T. whipplei was 25.51% in 98 stool samples analysed. Prevalence in HIV positive patients was significantly higher than in HIV-negative (33.8% vs. 9.09%, p = 0.008). Prevalence in the control group with no associated diseases was 20%, whereas no positive samples were observed in HIV-negative patients with MS, or in those diagnosed with CFS. The prevalence observed in HIV-positive patients without MS was 3035%, and with MS it was 55.5%. The number of positive samples varies depending on the primers used, although no statistically significant differences were observed. Conclusions: There is a high prevalence of asymptomatic carriers of T. whipplei among healthy and in HIV infected people from Spain. The role of T. whipplei in HIV patients with MS is unclear, but the prevalence is higher than in other populations. (C) 2015 Elsevier Espana, S.L.U. and Sociedad Espariola de Enfermedades Infecciosas y Microbiologia Clinica. All rights reserved.