Background: For normalization of displaced anatomical structure by large cyst, two-step procedure (decompression and enucleation afterward) has been recommended. However, the histological transformation after cystotomy for decompression was shown frequently in secondary enucleation. Therefore, analyses about effects and histological changes after decompression have been necessary. Methods: 48 cases diagnosed as large odontogenic cyst in the jaw and treated by decompression and secondary enucleation were retrospectively analyzed in clinical, rediographical, and histological aspects. Results: In dentigerous cyst, decompression was much useful. Impacted permanent teeth were erupted and reduction rate was higher than that of odontogenic keratocyst (OKC) and apical periodontal cyst. In OKC, among the 29 cases, 11 cases showed no-keratosis, proliferation and rete-ridge elongation after decompression. 4 cases showed no-keratosis, only. 7 cases showed orthokeratosis and rete-ridge elongation and 6 cases showed reteridge elongation, only. 1 case had no change. And the recurrence rate for OKCs was 10.3%. For all odontogenic cysts in this study, dysplasia was not found in cystic lining after decompression. Conclusions: This study implied that decompression for large odontogenic cyst was useful treatment modality because it was conservative treatment and recurrence rate was low although long treatment period was required.