BACKGROUND: Interpretation of medical images for the diagnosis and treatment of complex diseases from high-dimensional and heterogeneous data remains a key challenge in transforming healthcare. In the last few years, both supervised and unsupervised deep learning achieved promising results in the area of medical image analysis. Several reviews on supervised deep learning are published, but hardly any rigorous review on unsupervised deep learning for medical image analysis is available. OBJECTIVE: The objective of this review is to systematically present various unsupervised deep learning models, tools, and benchmark datasets applied to medical image analysis. Some of the discussed models are autoencoders and their variants, Restricted Boltzmann Machines (RBM), Deep Belief Networks (DBN), Deep Boltzmann Machine (DBM), and Generative Adversarial Network (GAN). Future research opportunities and challenges of unsupervised deep learning techniques for medical image analysis are also discussed. CONCLUSION: Currently, interpretation of medical images for diagnostic purposes is usually performed by human experts that may be replaced by computer-aided diagnosis due to advancement in machine learning techniques, including deep learning, and the availability of cheap computing infrastructure through cloud computing. Both supervised and unsupervised machine learning approaches are widely applied in medical image analysis, each of them having certain pros and cons. Since human supervisions are not always available or are inadequate or biased, therefore, unsupervised learning algorithms give a big hope with lots of advantages for biomedical image analysis.