Aim To compare clinical outcomes of 'extra-short' and regular bone level implants in the posterior maxilla for 12 months after loading. Materials and Methods Twenty-three systemically healthy, non-smoking patients received 30 extra-short, 24 regular bone level implants. Acrylic stents were fabricated for each patient for correct implant positioning. Implant lengths were 4-6 mm in the test, 8/10 mm in the control group. Radiographic evaluation was performed at baseline, 6, and 12 months after loading. Crestal bone level (CBL), CBL change (CBLC), true crown length (TCL), implant/crown ratio (ICR) and residual bone height (RBH) below maxillary sinus floor were calculated digitally. Data were tested statistically. Results Residual bone height was significantly lower, and TCL and ICR were higher in the test than the control group (P < 0.0001). CBL measurements at baseline were 0.19 +/- 0.18 mm and 0.31 +/- 0.37 mm and at 12 months, 0.24 +/- 0.24 mm and 0.41 +/- 0.31 mm, respectively in the test and control groups. CBL values at 12 months were significantly lower in the test than the control group (P < 0.05). CBLCs were similar at all times (P > 0.05). No correlation was found between the CBLC and implant/prosthetic parameters. Conclusion Extra-short and regular implants might provide similar clinical outcomes in prosthetic rehabilitation of atrophic maxilla, during 12 months follow-up.