Objective: the aim of this study was to compare the marginal bone loss between mini-implants and short length implants in patients rehabilitated with implant retained mandibular complete overdenture.Material and methods: Fourteen completely edentulous male patients were selected from those attended the out-patient clinic of Removable Prosthodontic Department, Faculty of Dentistry-Ain Shams University to participate in this study. Based on the cone beam computed tomographic (CBCT) assessment, the selected patients were divided into two equal groups: Group (I): Patients received conventional complete maxillary dentures opposed by mandibular overdentures supported and retained by four Mini-implants of 2.5mm diameter and 12 mm length in the interforaminal region. Group (II): Patients received conventional complete maxillary dentures opposed by mandibular overdentures supported and retained by two conventional short implants of 4mm diameter and 8mm length placed in the lateral-canine regions. CBCT records were obtained upon Overdenture Insertion (Baseline), Six Months, Twelve Months after insertion.The Mesial, Distal, Buccal and Lingual marginal bone heights around the implants were evaluated, using the linear measurement system of the software with flat panel detector supplied by the cone beam CT. Results: Peri-Implant Bone Loss in Group (I):At six months following denture insertion calculated means of the measured bone loss for the Mesial surfaces were 0.5±0.1 mm, for the Distal surfaces were 0.55±0.03 mm ,for the Buccal surfaces were 0.50±0.12 mm and for the Lingual surfaces were 0.49±0.03mm.The calculated means of the measured bone loss was statistically significant at P < 0.05. At twelve months following denture insertion, the calculated means of the measured bone loss for the Mesial surfaces were 0.78±0.1 mm, for the Distal surfaces were 0.92±0.7 mm, for the Buccal surfaces were 0.79±0.1mm and for the lingual surface 0.74±0.03mm. The calculated means of the measured bone loss were statistically significant (P ≤ 0.05). Peri-Implant Bone Loss in Group (II): At six months following denture insertion calculated means of the measured bone loss for the Mesial surfaces were 0.56 ± 0.07 mm,for the Distal surfaces were 0.67 ± 0.06 mm,for the Buccal surfaces were 0.56 ± 0.06 mm and for the Lingual surfaces were 0.55 ± 0.05mm.The calculated means of the measured bone loss were statistically significant at P < 0.05. At twelve months following denture insertion calculated means of the measured bone loss for the Mesial surfaces were 0.7 ± 0.07 mm,for the Distal surfaces were 0.87 ± 0.07 mm,for the Buccal surfaces was 0.7 ± 0.08 mm and for the Lingual surfaces were 0.74 ± 0.007 mm. The calculated means of the measured bone loss were statistically significant ( P ≤ 0.05).The calculated means of the measured bone loss in group I of mini implants were higher than group II of short implants for the Mesial, distal,buccal and lingual surfaces and over all bone loss at 6 months and 12 months but was found statistically insignificant ( P ≤ 0.05).Conclusions: Within the limitation of this study, it could be concluded that marginal bone loss around mini implants supporting and retaining mandibular complete overdenture is higher than the marginal bone loss around conventional short implants supporting and retaining mandibular complete overdenture although the difference was statistically insignificant.