Purpose: To evaluate whether 6 mm long × 4 mm wide dental implants could be an alternative to implants of at least 10 mm long placed in bone augmented with bone substitutes in posterior atrophic jaws. Materials and methods: A total of 20 patients with bilateral atrophic mandibles, and 20 patients with bilateral atrophic maxillae, having 5 mm to 7 mm of bone height below the maxillary sinus or 6 mm to 8 mm above the mandibular canal, had their side of the jaws randomly allocated according to a split-mouth design. They were allocated to receive one to three 6 mm long × 4 mm wide implants, or implants of at least 10 mm long in augmented bone by two different surgeons at different centres. Mandibles were vertically augmented with interpositional equine bone blocks and resorbable barriers, and implants were placed 3 months later. Maxillary sinuses were augmented with particulated porcine bone via a lateral window and implants were placed simultaneously. After 4 months, all implants were submerged and loaded with provisional prostheses. Four months later, definitive prostheses were delivered. Outcome measures were prosthesis and implant failures, any complication and radiographic peri-implant marginal bone level changes. Results: Five patients (three treated in mandibles and two in maxillae) dropped out before the 3-year post-loading follow-up. Two short maxillary implants affected by peri-implantitis failed together with their prosthesis vs three mandibular prostheses that could not be placed on implants at least 10 mm long due to graft failures; one was associated with the loss of three implants because of infection. There were no statistically significant differences in implant (difference in proportions = 0.000; 95% CI: -0.140 to 0.140; P = 1.000) and prosthesis failures (difference in proportions = 0.057; 95% CI: -0.094 to 0.216; P = 0.625). In total, 18 complications occurred in 13 patients at augmented sites vs four complications in three patients with 6 mm long implants. Significantly more complications occurred at grafted sites in mandibles (difference in proportions = 0.353; 95% CI: 0.005 to 0.616; P = 0.031), but not in maxillae (difference in proportions = 0.222; 95% CI: -0.071 to 0.486; P = 0.219). In mandibles, patients with 6 mm long implants lost an average of 1.25 mm of peri-implant bone at 3 years vs 1.54 mm in patients with implants of at least 10 mm long. The difference was statistically significant (mean difference = 0.29 mm; 95% CI: 0.08 to 0.51 mm; P = 0.010). In maxillas, patients with 6 mm-long implants lost an average of 1.28 mm of peri-implant bone at 3 years vs 1.50 mm in patients with implants of at least 10 mm long. The difference was statistically significant (mean difference = 0.22 mm; 95% CI: 0.08 to 0.35 mm; P = 0.003). Conclusions: Results at 3 years after loading indicate that 6 mm long implants with a conventional diameter of 4 mm achieved similar, if not better, results than longer implants placed in augmented bone. Short implants might be a preferable choice to bone augmentation, especially in posterior mandibles, since the treatment is faster, cheaper and associated with less morbidity. However, data obtained 5 to 10 years after loading are necessary before making reliable recommendations.