Background Functional somatic symptoms (FSS) are bodily complaints of unclear etiology, which are (currently) not fully explained by well-recognized somatic pathology. Doctors are often hesitant to diagnose FSS, due to the risk to miss a somatic disease. The purpose of this study is to review available literature on the percentage of patients diagnosed with FSS reported to have an underlying somatic disease that explains their symptoms previously labeled as FSS. Methods We performed a systematic search of Medline, Embase and PsycINFO databases and reference lists of selected articles. We included studies published between January 1980 and July 2014 without language restrictions. Studies that measured the percentage of underlying somatic diseases after a diagnostic evaluation or naturalistic follow-up period in adult patients initially diagnosed with FSS were included. As primary outcome measure the weighted percentage of revised diagnoses was calculated using meta-analyses. Results Six diagnostic evaluation studies (total N =1804 patients) and 16 follow-up studies (total N =2440 patients) were included. The percentage of revised diagnosis in patients initially diagnosed with FSS was 8.8% (95% CI 1.0 to 22.2, p =0.007) in diagnostic evaluation studies and 0.5% (95% CI 0.01 to 1.5, p =0.03) in follow-up studies. Partially or possibly related diagnoses were rarely found. No specific somatic diagnosis seemed to be missed systematically. Conclusions The percentage of underlying somatic diseases in patients previously diagnosed with FSS is relatively small but unneglectable.