Purpose: To evaluate whether 6-mm-long by 4-mm-wide dental implants could be an alternative to implants 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 to 7 mm of bone height below the maxillary sinus or 6 to 8 mm above the mandibular canal, had their sides of the jaws randomly allocated according to a split-mouth design. They were allocated to receive one to three 6-mm-long and 4-mm-wide implants, or implants at least 10-mm long in augmented bone by two different surgeons in 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. All implants were submerged and loaded, after 4 months, 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. The follow-up was 5 years after loading for all patients. Results: Eight patients (five treated in mandibles and three in maxillae) dropped out before the 5-year post-loading follow-up. Four short implants (two maxillary and two mandibular) affected by peri-implantitis failed together with their prostheses versus three mandibular prostheses which 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 (P = 1.0) and prosthesis failures (P = 1.0). In total, 19 complications occurred in 14 patients at augmented sites versus five complications in four patients with 6-mm-long implants (P = 0.118). More complications occurred at grafted sites both in mandibles (P = 0.727), and maxillae (P = 0.063), although the differences were not statistically significant. In mandibles, patients with 6-mm-long implants lost an average of 1.34 ± 0.35 mm of peri-implant bone at 5 years versus 2.11 ± 0.59 mm in patients with implants at least 10-mm long. The difference was statistically significant (mean difference = 0.77 ± 0.70 mm; 95% CI: 0.32 to 1.21 mm; P = 0.003). In maxillae, patients with 6-mm-long implants lost an average of 1.52 ± 0.47 mm of peri-implant bone at 5 years versus 1.85 ± 0.51 mm in patients with implants at least 10-mm long. The difference was statistically significant (mean difference = 0.33 ± 0.36 mm; 95% CI: 0.14 to 0.53 mm; P = 0.002). Conclusions: Results at 5 years after loading indicate that 6-mm-long implants with a conventional diameter of 4 mm achieved similar results to longer implants placed in augmented bone. Short implants might be a preferable choice to bone augmentation, especially in posterior mandibles since the treatment was faster, cheaper and associated with less morbidity. However, 10-year post-loading data are necessary before making reliable recommendations.