Arterial Spin Labeling (ASL) enables quantitative measurement of myocardial blood flow (MBF) by averaging over multiple ASL pairs providing a voxelwise map in units of milliliters of blood per gram of tissue per minute (ml/g/min). However, its estimation accuracy in free breathing acquisitions depends critically on the quality of the image registration algorithm. In this work, a groupwise non-rigid registration method with a similarity measure based on Principal Component Analysis (PCA) was applied to ASL images of the heart acquired during free breathing. The method was compared against a pair-wise registration algorithm provided by the advanced normalization tools software (ANTs). Results demonstrate the feasibility of using PCA-groupwise for temporal ASL image registration.