BackgroundThe treatment of medium-sized odontogenic jaw cysts is inconsistent at present. Two main treatments, namely decompression and enucleation, are used overlappingly. This retrospective analysis aims to provide useful references for technique selection for future management of medium-sized odontogenic jaw cysts. MethodsOdontogenic cysts with lesion sizes ranging 2–4 cm were included. The clinical and radiological data of the patients were reviewed. Decompression-first and direct enucleation treatments were the two main surgical techniques. The preoperative parameters and postoperative outcomes were compared between the two groups. ResultsOut of 69 patients included, 40 (58 %) were in the decompression group and 29 (42 %) in direct enucleation group. The logistic regression analysis of preoperative parameters demonstrated that the maximum lesion size and the chief surgeon's preference could affect the selection of surgical techniques for medium-sized cysts (P < 0.05). Receiver operating characteristic curve analyses demonstrated that a lesion size >2.5 cm was the best cutoff value for predicting a decompression selection. Most postoperative outcomes differed significantly between the two groups (P < 0.05). Lower-risk anesthesia, shorter hospitalization, tooth function protection, and fewer neurosensory impairments were decompression-favoring outcomes. However, more follow-up visits, more postoperative X-rays, and longer postoperative care were outcomes against decompression. The recurrence rate was low and did not differ significantly between the two groups (P > 0.05). ConclusionsThere is no apparent preference for treating medium-sized jaw cysts. The maximum lesion size is a moderate-impact factor for treatment selection. A tendency to prefer decompression-first with larger lesion size was found in medium-sized jaw cysts. The advantages of teeth preservation and low neurosensory impairment of decompression were verified in the medium-size jaw cysts. The burden of postoperative care should be considered when selecting decompression.