Autonomy is a buzz-word in current A-Life, and in some other areas of cognitive science too. And it is generally regarded as a Good Thing. However, neither the spreading use nor the growing approval have provided clarity. This Special Issue of BioSystems is devoted to clarifying the concept, and to showing how it is being used in various examples of empirical research. Given the obscurity that still attends the concept, however, we should not expect to find that all the ‘clarifications’ are equivalent – or even mutually consistent. Similarly, we should not expect to find that the notion is applied identically in all the research that is reported here. So this preliminary sketch of the conceptual landscape may be helpful.