Femorotibial alignment is an important factor affecting patient outcome after total knee arthroplasty (TKA). It was the aim of this study to report our first results using a CT-based navigation system in two-stage revision surgery for infected TKA. Two patients with chronic deep infection after primary TKA underwent two-stage revision arthroplasty with temporary articulating cement spacers followed by prosthesis re-implantation using a CT-based navigation system. Postoperative radiographs showed accurate alignment of the femoral and tibial components. CT-based navigation systems offer the opportunity for preoperative planning and accurate intra-operative navigation of cutting blocks. They can be considered of value for primary TKA but even more so for two-stage revision arthroplasty.