Purpose: To evaluate whether 5-mm short dental implants could be an alternative to augmentation with anorganic bovine bone and placement of at least 10-mm long implants in posterior atrophic jaws. Materials and methods: Fifteen patients with bilateral atrophic mandibles (5 mm to 7 mm bone height above the mandibular canal) and 15 patients with bilateral atrophic maxillae (4 mm to 6 mm bone height below the maxillary sinus), and bone thickness of at least 8 mm, were randomised according to a split-mouth design to receive one to three 5-mm short implants or at least 10-mm long implants in augmented bone. Mandibles were vertically augmented with interpositional bone blocks and maxillary sinuses with particulated bone via a lateral window. Implants were placed after 4 months, submerged and loaded, after another 4 months, with provisional prostheses. Four months later, definitive provisionally cemented prostheses were delivered. Outcome measures were: prosthesis and implant failures; any complication and peri-implant marginal bone level changes. Results: In five augmented mandibles, the planned 10-mm long implants could not be placed and shorter implants (7 mm and 8.5 mm) had to be used instead. Three years after loading, two patients, one treated in the mandible and one in the maxilla, dropped out. Three prostheses (1 mandibular and 2 maxillary) failed in the short implant group versus none in the long implant group. In mandibles, one long implant failed versus two short implants in 1 patient. In maxillae, one long implant failed versus three short implants in 2 patients. There were no statistically significant differences in the failures. Eight patients had 13 complications at short implants (1 patient accounted for 6 complications) and 11 patients had 13 complications at long implants. There were no statistically significant differences in complications (P = 0.63, difference = 0.10, 95% CI from -0.22 to 0.42). Three years after loading, patients with mandibular implants lost on average 1.44 mm at short implants and 1.63 mm at long implants of peri-implant marginal bone. This difference was not statistically significant (difference = 0.24 mm; 95% CI -0.01, 0.49 P = 0.059). In maxillae, patients lost on average 1.02 mm at short implants and 1.54 mm at long implants. This difference was statistically significant (difference = 0.41 mm; 95% CI 0.21, 0.60, P = 0.001). Conclusions: Three years after loading, 5-mm short implants achieved similar results as longer implants in augmented bone. Short implants might be a preferable choice to vertical bone augmentation, especially in mandibles, since the treatment is faster and cheaper, however there are still insufficient data on the long-term prognosis of short implants.