The axis of rotation in biomechanics is a major tool to investigate joint function; therefore, many methods to estimate the axis of rotation have been developed. However, there exist several problems to describe, estimate, and test the axis statistically. The axis is directional data(axial data) and it should not be analyzed with traditional statistics. A proper comparative method should be considered to compare axis estimating methods for the same given data ANOVA (analysis of variance) is a frequently used statistical method to compare treatment means in experimental designs. In case of the axial data response assumed to come from Watson distribution, there are a few ANOVA method options. This study constructed ANOVA models for within-subjects designs of axial data. Two models (one within-subjects factor and two within-subjects factors crossed design) were considered. The empirical data used in this study were instantaneous axes of rotation of flexion/extension at the knee joint and the flexion/extension and pronation/supination at the elbow joint. The results of this study can be further applied to the various analysis of experimental designs.