The primary goal of this study was to identify and quantify indications for retaining third molars. This retrospective cohort study included 1682 patients (818 male, 864 female; mean age 31 years) who were referred to the University Hospitals Leuven for third molar removal. Eight reasons for retaining the third molars were identified: (1) risk of damaging adjacent structures, (2) compromised health status, (3) adequate space for eruption, (4) third molar serves as abutment tooth, (5) orthodontic reasons, (6) eruption into proper occlusion, (7) symptomless third molars in patients >30 years old, and (8) patient preference. To compare these categories between sex and age groups, a generalized linear model for binary data was fitted with a logit link. A total of 1149 third molars in 548 patients were not extracted. The most frequent reasons for retaining third molar teeth were: eruption into proper occlusion (31.9%), patient preference (31.5%), and symptomless third molars in patients >30 years old (17.5%). Compromised health status and advanced age were often included in the decision regarding whether to retain the third molars. One third of the referred patients had reasons to retain one or more third molars. These findings might facilitate the future development of a consensus statement.