Total knee arthroplasty (TKA) is a frequently performed procedure in orthopaedic surgery. Recently, patient-specific instrumentation was introduced to facilitate correct positioning of implants. The aim of this study was to compare the early clinical results of TKA performed with patient-specific CT-based instrumentation and conventional technique. A prospective, randomized controlled trial on 112 patients was performed between January 2011 and December 2011. A group of 112 patients who met the inclusion and exclusion criteria were enrolled in this study and randomly assigned to an experimental or control group. The experimental group comprised 52 patients who received the Signature CT-based implant positioning system, and the control group consisted of 60 patients with conventional instrumentation. Clinical outcomes were evaluated with the KSS scale, WOMAC scale, and VAS scales to assess knee pain severity and patient satisfaction with the surgery. Specified in-hospital data were recorded. Patients were followed up for 12 months. At one year after surgery, there were no statistically significant differences between groups with respect to clinical outcomes and in-hospital data, including operative time, blood loss, hospital length of stay, intraoperative observations, and postoperative complications. Further high-quality investigations of various patient-specific systems and longer follow-up may be helpful in assessing their utility for TKA.