Identifying a submandibular (Wharton's) duct punctum often hinders sialendoscopy; however, there is a paucity of evidence on whether the appearance of Wharton's duct papilla impacts the sialendoscopic procedure. A classification of Wharton's duct papillae based on the macroscopic appearance, size of dilatation probes, and sialendoscopic approach was proposed herein. The classification describing four main types of papillae, A, B, C, and D, was prospectively evaluated on 351 Wharton's duct papillae in 315 patients. For each papillae type, the demographic/clinical data, intraoperative complications, and time required for sialendoscope introduction were analyzed. Estuary-like papilla (type A) was commonly seen after spontaneous stone extrusion, had no intraoperative complications noted, and had the shortest time required for the sialendoscope introduction. Normal papilla (type B) was the most frequently observed papilla (48.1%), reflecting diverse underlying pathology, while difficult papilla (type C) was often associated with unfavorable anatomical variations of the mandible or floor of the mouth. Substantially closed papilla (type D) had the highest rate of intraoperative complications, namely, perforation with a false passage, and required the longest time for the sialendoscope introduction. In seven patients (2.0%), the entrance into the duct was feasible only through the fistula, while the sialendoscope introduction failed in eight patients (2.3%). In conclusion, the appearance of Wharton's duct papillae may be influenced by the underlying pathology. Based on the proposed classification, papilla typology affects the duration of sialendoscope introduction and may influence the frequency of intraoperative complications.