The paper provides an overview of the development of intelligent data analysis in medicine from a machine learning perspective: a historical view, a state-of-the-art view, and a view on some future trends in this subfield of applied artificial intelligence. The paper is not intended to provide a comprehensive overview but rather describes some subareas and directions which from my personal point of view seem to be important for applying machine learning in medical diagnosis. In the historical overview, I emphasize the naive Bayesian classifier, neural networks and decision trees. I present a comparison of some state-of-the-art systems, representatives from each branch of machine learning, when applied to several medical diagnostic tasks. The future trends are illustrated by two case studies. The first describes a recently developed method for dealing with reliability of decisions of classifiers, which seems to be promising for intelligent data analysis in medicine. The second describes an approach to using machine learning in order to verify some unexplained phenomena from complementary medicine, which is not (yet) approved by the orthodox medical community but could in the future play an important role in overall medical diagnosis and treatment.