The purpose of this retrospective study was to evaluate the 4-year outcome of endodontic microsurgery using two different magnification devices. One-hundred and two teeth in 65 patients were included according to specific selection criteria. Endodontic surgery was performed under surgical microscope as magnification device in 63 teeth in 36 patients, while 39 teeth in 29 patients were treated under magnifying loupes. Thirteen patients did not attend the 4-year follow up. The overall success rate on a patient basis was 91.7% at the 1-year and 90.5% at the 4-year follow up for the group using loupes, while for the group using microscope it was 91.4% at the 1-year and 93.3% at the 4-year follow up. The relative risk was 2.07 (95% confidence interval: 0.31, 13.95) in favour of the group in which microscope was used. No statistically significant difference was found in the treatment outcomes relating to the type of magnification device.