Alignment of time series is an important problem to solve in many scientific disciplines. In particular, temporal alignment of two or more subjects performing similar activities is a challenging problem due to the large temporal scale difference between human actions as well as the inter/intra subject variability. In this paper we present canonical time warping (CTW), an extension of canonical correlation analysis (CCA) for spatio-temporal alignment of the behavior between two subjects. CTW extends previous work on CCA in two ways: (i) it combines CCA with dynamic time warping for temporal alignment; and (ii) it extends CCA to allow local spatial deformations. We show CTWs effectiveness in three experiments: alignment of synthetic data, alignment of motion capture data of two subjects performing similar actions, and alignment of two people with similar facial expressions. Our results demonstrate that CTW provides both visually and qualitatively better alignment than state-of-the-art techniques based on dynamic time warping.