A 7-year-old boy presented with a periodontal problem related to an erupting lower molar. The tooth showed a 15 mm deep periodontal pocket on the buccal aspect. A microbiological DNA test excluded a periodontal origin. The treatment consisted of local antimicrobial therapy and cleaning and filling of the pocket with Atridox. 2 years after therapy the pocket completely disappeared. Finding periodontal pockets on freshly erupted teeth with acute symptoms should suggest the diagnosis of a cyst. This could prevent surgical endodontal or periodontal therapy. This problem can be managed effectively with minimal therapy and local antibiotics.