Implant therapy for tooth loss in the molar area is challenging due to the anatomical limitations, requiring bone augmentation procedures that are associated with high surgical complexity and long postsurgical recovery. Recently, many studies have demonstrated the usefulness of short implants. However, few studies have been performed in Japanese patients to evaluate peri-implant bone changes, changes in peri-implant epithelial tissue, and patient satisfaction. The present study included 16 patients (5 men, 11 women; mean age: 60 years) who received 26 short (6-mm) implants. Changes in peri-implant bone and epithelial tissue were measured radiographically at superstructure loading and after 2 years. Peri-implant pocket probing depth was measured at the epithelial tissue and compared at both time points. Patient satisfaction was graded using the Oral Health Impact Profile (OHIP-14) before treatment and at follow-up. The mean mesial and distal bone levels were -0.05 mm and 0.37 mm at loading, respectively, and were 0.33 mm and 0.53 mm after 2 years, respectively. Significant peri-implant bone formation for mesial and distal bone levels at both time points were determined by Wilcoxon signed-rank test. Mean probing depth increased slightly, from 3.03 mm at loading to 3.33 mm after 2 years, but no significant difference was found. The OHIP-14 found that patient satisfaction levels increased after 2 years. Using 6-mm short implants in sites with insufficient bone levels can be a highly beneficial treatment option for patients, as it avoids the need for bone augmentation. However, more long-term and detailed studies on the clinical outcomes for these implants are required.