We aimed to establish the characteristics and potential etiological risk factors of eruption disturbances in mandibular second molars (MM2). We retrospectively enrolled patients with eruption disturbances in MM2. A total of 143 MM2 with eruption disturbances from 112 patients (mean age 17.45 ± 6.35) were included in this study. Panoramic radiographs were employed to determine the risk factor, angulation type, impaction depth, tooth development stage, and associated pathology. The novel classification method of MM2 was based on impaction depth and angulation. Of 143 MM2, 137 and 6 were diagnosed with impaction and retention, respectively. Insufficient space was the most frequent risk factor for eruption disturbances. There were no significant differences between retention and impaction regarding sex, age, or side. The most frequent impaction type was Type I. The most frequent angulation of impacted MM2 was mesioangular. Impacted MM2 with shallower depth were more frequently associated with the presence of first molar undercut. Impaction types did not differ according to age, side, development stage, or distance from the MM1 distal surface to the anterior border of the ramus. Dentigerous cysts were associated with earlier MM2 development stages and greater MM2 depth. In conclusion, MM2 impaction types differed according to the risk factor, angulation type, MM1 undercut, and presence of cysts. Early MM2 development stage and greater MM2 depth were risk factors for MM2 eruption disturbances with cysts.