The historical start of self-organizational thinking can be traced back to Aristotle’s four cause theory. The Stagirite did not limit his understanding of the world to the material, formal and efficient causes but was ingenious enough to stress the importance of the final goal, final condition of any process that is not a stagnated state but rather a dynamic situation of openness to self-organization. The Aristotelian approach to the understanding of the world was suppressed at the dawn of modern science by Francis Bacon and René Descartes. Isaac Newton seemed to follow the newly established tradition. We must not forget, however, that Newton was not a seeker for scientific knowledge in the narrow sense. His real aspiration was directed to creating a holistic picture of physical reality. That’s why he called his main treatise ‘Natural Philosophy’. It was Newton who initiated an active experimental dialogue with nature that developed into self-organizational thinking in modern science. The next important step was taken by the so-called philosophes of the Enlightenment who were not happy with the concentration of scientific research on stable systems and neglecting attention to developing structures, including everything connected with life. The term ‘self-organization’, however, came into use only after World War II. It was coined by the psychiatrist and engineer W. Ross Ashby. It became associated with cybernetics until Ilya Prigogine gave it a whole new meaning. Attention was shifted from cybernetics to thermodynamics. It was Prigogine who made the idea of self-organization the core of his new approach to science, first in chemistry and physics, when in social science as well. Prigogine’s approach to science, based on self-organization theory was taken as revolutionary by some philosophers of science. At the same time, he has been severely criticised by many. Today, it is a normal part of our thinking as scientists that there are self-organizing systems all around us. It may well be that the essence of the Prigoginian “revolution” has not been fully understood yet. We are witnessing new attempts to achieve a united understanding of the human matters on the basis of science. Nicholas Maxwell is even speaking about the need for a “New” Enlightenment. Thus, the idea of self-organization deserves taking a fresh look at.