The purpose of this study was to analyze the value of different diagnostic methods in detecting the primary site and the impact of primary tumors on the clinical outcome of carcinoma of unknown primary (CUP). In this multicenter, retrospective study, 124 patients with true CUP (n = 94) and CUP turned to primary carcinoma (n = 30) were included. Patients with evidence of primary site during the clinical examination were excluded a priori. The diagnostic procedure was comprised of imaging and invasive methods (fine-needle-aspiration, tonsillectomy and panendoscopy). All patients were treated with curative intent. Despite extensive diagnostic workup, the primary site remained unknown in 75.8%. Invasive diagnostic methods showed higher primary detection rates than imaging modalities (15.1% vs. 7.8%). Tonsillectomy and panendoscopy revealed the primary tumor in 14.9% and 15.2% of patients, whereas the detection rates of CT, MRI and FDG-PET-CT were 10.1%, 4.8% and 6.5%, respectively. The occurrence of primary tumors led to a significantly deteriorating 5-year overall survival (p = 0.002) and emerged as survival prognosticator (HR = 2.764, p = 0.003). Clinical examination in combination with tonsillectomy and panendoscopy was superior to imaging alone in detecting the primary tumor. When the CUP of patients turned to a primary tumor, clinical outcome was significantly worse than in CUP patients.