Background: Periodontitis is primarily a bacteria-induced disease that can be modified by tooth-related local factors. Cervical enamel projections (CEPs) are a common tooth anomaly that can act as a contributing factor in the development of periodontitis. They are most commonly found at the buccal surfaces of mandibular molars. Methods: A 57-year-old female was referred to our clinic for treatment of chronic periodontitis. Clinical examination revealed moderate attachment loss that was localized to the palatal side of the maxillary secondary molars. The rest of the dentition was less affected, with a diagnosis of generalized slight chronic periodontitis. Initial non-surgical periodontal treatment was provided, followed by apically positioned flap surgery in the maxillary right and left posterior areas. At the time of surgery, CEPs were found where the periodontium was most affected. Results: Due to the fact that surgical intervention exposed the CEPs, they were not removed. After the active therapy, which resulted in inflammation resolution and maintainable probing depth, the patient was placed on a three-month recall for periodontal maintenance. Conclusions: This case report presents CEPs in an unusual location in the palatal roots of maxillary secondary molars. CEPs confirm their role as a local contributing factor in localized chronic periodontitis.