The primary cilium is a small sensory organelle that is required for different aspects of embryonic development, including the formation of the heart. The structure and composition of cilia have been extensively studied, so that several markers of primary cilia have now been identified. However, the role of cilia in specific cell types remains poorly understood. We describe here a series of approaches to image primary cilia in the rodent heart or in primary cultures of cells dissociated from the heart. As the cilium is a marker of cell polarity, we also provide, for quantitative image analysis of cilium orientation, tools which are generally applicable to other types of tissues.