The measurement and evaluation of spindle errors is an important task in the assessment of the accuracy of machine tools. The commonly followed capacitive-sensor-based measurement technique requires a comprehensive error separation method for the identification of the unwanted contributions of centering error, the form error of the artifact and thermal drift. This paper presents a method for form error separation that is suitable for the evaluation of the radial error of high-speed spindles. In the present work, a fixed sensitive radial error motion test is conducted using a capacitive sensor and a cylindrical artifact at different spindle speeds. A mathematical model consisting of a second-order polynomial and Fourier series function is used to interpret the data measured in the time domain. The form profile of the artifact is measured separately in a roundness tester using a capacitive sensor. A harmonic analysis method is proposed to identify and separate the dominant harmonic components in the form profile of the artifact. A mathematical description of the proposed method is described and experimental results are presented. Application of the proposed method to the evaluation of the synchronous radial error of a high-spindle is provided for measured data. The proposed method analyzes the data measured in the time domain and is suitable for the identification of the spindle errors at high-speed conditions.