Background Imaging of the salivary ductal system is relevant prior to an endoscopic or a surgical procedure. Various imaging modalities can be used for this purpose. The aim of this study was to compare the diagnostic capability of three-dimensional (3D)-cone-beam computed tomography (CBCT) sialography versus magnetic resonance (MR) sialography in non-tumorous salivary pathologies. Methods: This prospective, monocenter, pilot study compared both imaging modalities in 46 patients (mean age 50.1 ± 14.9 years) referred for salivary symptoms. The analyses were performed by two independent radiologists and referred to identification of a salivary disease including sialolithiasis, stenosis, or dilatation (primary endpoint). The location and size of an abnormality, the last branch of division of the salivary duct that can be visualized, potential complications, and exposure parameters were also collected (secondary endpoints). Results Salivary symptoms involved both the submandibular (60.9%) and parotid (39.1%) glands. Sialolithiasis, dilatations, and stenosis were observed in 24, 25, and 9 patients, respectively, with no statistical differences observed between the two imaging modalities in terms of lesion identification (p 1 = 0.66, p 2 = 0.63, and p 3 = 0.24, respectively). The inter-observer agreement was perfect (> 0.90) for lesion identification. MR sialography outperformed 3D-CBCT sialography for visualization of salivary stones and dilatations, as evidenced by higher positive percent agreement (sensitivity) of 0.90 [95% CI 0.70–0.98] vs. 0.82 [95% CI 0.61–0.93], and 0.84 [95% CI 0.62–0.94] vs. 0.70 [95% CI 0.49–0.84], respectively. For the identification of stenosis, the same low positive percent agreement was obtained with both procedures (0.20 [95% CI 0.01–0.62]). There was a good concordance for the location of a stone (Kappa coefficient of 0.62). Catheterization failure was observed in two patients by 3D-CBCT sialography. Conclusions: Both imaging procedures warrant being part of the diagnostic arsenal of non-tumorous salivary pathologies. However, MR sialography may be more effective than 3D-CBCT sialography for the identification of sialolithiasis and ductal dilatations. Trial registration NCT02883140.