Objectives: To compare the overall diagnostic outcomes of 3D-CBCT sialography and ultrasonography (US) in the detection of sialolithiasis, ductal dilatation, and ductal stenosis. Methods: This retrospective monocentric study compared the two imaging modalities carried out in the same patients referred for salivary symptoms of the parotid and submandibular glands. The primary endpoint was the capacity of the imaging procedure to diagnose a lesion. The secondary objectives were the detection rates according to the type of lesion, analysis of the causes of failure, and the parameters of radiation exposure and safety (for 3D-CBCT sialography). Results: Of the 236 patients who received a 3D-CBCT sialography in our institution, 157 were ultimately included in the per-protocol analysis. 3D-CBCT sialography allowed detection of ductal lesions in 113 patients versus 86 with US. The two imaging modalities yielded congruent interpretations in 104 out of 157 subjects (66.2%). Higher sensitivity and negative predictive value were observed with 3D-CBCT sialography compared with US, irrespective of the lesions studied: 0.85 vs 0.65 and 0.70 vs 0.44, respectively. Regarding the sialolithiasis, both 3D-CBCT sialography and US allowed identification of lesions with high sensitivity and negative predictive value (0.80 vs 0.75 and 0.88 vs 0.78, respectively). Conclusions: US remains the first-line examination for exploration of the salivary lesions. 3D-CBCT sialography is an alternative in case of inconclusive US, and prior to any endoscopic procedure.