Fever of intermediate duration (FID) is a new nosologic entity defined as fever higher than 38 degrees C that has a duration of between 1 and 4 weeks and that after an initial approach has not been diagnosed. It has clinical similarities with fever of unknown origin, but because of characteristic etiologies it requires the term FID. We describe the clinical characteristics and etiology of FID in the south of Spain and create a treatment algorithm. Retrospective study of the medical charts of patients attending at our Service during 2000 and 2005 who had an initial diagnosis of FID and who had a complete follow-up until the resolution of symptoms. Two hundred and thirty-three patients met the inclusion criteria, of whom 164 were men. Median number of days before being referred to our service was 9 (range 2-28). Half of the patients had elevation of transaminases, and CRP and ESR were slightly elevated, 2.8 mg/dl (range 0.1-50) and 16 mm/h (range 1-131) respectively. A final diagnosis was made in 80 patients, with infection with coxiella (32 patients), CMV (16 patients), rickettsial species (11 patients), VEB virus (6 patients), and brucella (5 patients) being the more frequent entities. Doxycycline was the antibiotic most frequently prescribed. Among patients with Q fever, CMV, and rickettsial infection, the majority had abnormal hepatic function, (87%, 93%, and 55% respectively). In FID, a diagnosis is reached in a minority of patients, although the prognosis is excellent in most of them. In our patients the clinical picture of Q fever, CMV, and rickettsial infections included abnormal hepatic function. In addition, these three infections are the most frequently diagnosed so when treating a patient with FID, if elevation of liver enzymes is present patients should start on doxycycline.