This study was designed to compare the correlations between intraoperative navigation and radiographic alignment in patients who underwent total knee arthroplasty (TKA) and open wedge high tibial osteotomy (HTO). The reliability of navigation and radiographic alignment before and after surgery was compared in 82 prospectively enrolled patients who underwent open wedge HTO and 91 knees that underwent TKA. The absolute difference in preoperative mechanical axis (MA) between navigation and radiography was 1.1 degrees greater in the TKA than in the HTO group (2.6 vs. 1.5 degrees, p < 0.001). Postoperatively, however, the absolute difference between navigation and radiographic measurements of MA was 1 degree greater in the HTO than in the TKA group (2.4 vs. 1.4 degrees, p < 0.001). The percentage of outliers, defined as a >3 degrees difference between navigation and radiographic MA, was significantly greater preoperatively in the TKA group (37 vs. 10%, p < 0.001), but significantly greater postoperatively in the HTO group (28 vs. 10%, p < 0.001). The discrepancy between navigation and radiographic measurement of coronal alignment was significantly greater preoperatively in the TKA than in the HTO group, whereas the discrepancy was significantly greater postoperatively in the HTO group.