(1) Background: there are few studies on the inflammation of unknown origin (IUO). We sought to determine the etiologies and prognosis of IUO, as well as the contribution of complementary examinations. (2) Methods: this retrospective study analyzed patients meeting the Vanderschueren’s criteria in the Hospices Civils de Lyon from 2005 to 2020. (3) Results: a total of 57 patients (mean age: 67 years; interquartile range: 55–79) were included. Final diagnoses were made for 26 (46%) patients. Non-infectious inflammatory diseases were the most common diagnoses (13/26, 50%), followed by neoplasms (10/26, 38%; 8/10 hematological malignancies), infections (2/26, 8%), and miscellaneous causes (1/26, 4%). Moreover, 18-FDG-PET/CT was contributory in 12/42 cases. Anti-neutrophil cytoplasmic antibodies, serology, temporal biopsies, and bone marrow aspirates were contributory in 3/41, 1/57, 5/23, and 3/19 cases, respectively. At last follow-up (mean follow-up duration: 48 months), 8/31 undiagnosed patients were cured (five received an empirical treatment), and 5/31 died (one death was related to the empirical treatment). (4) Conclusion: more than half of the IUO remained undiagnosed. Non-infectious inflammatory diseases and hematological malignancies were the most common etiologies. Moreover, 18-FDG-PET/CT had the highest diagnostic value. Most IUO without final diagnosis persisted. The role of empirical treatments remains to be explored.