A large body of human epidemiological data, as well as experimental studies, suggest that environmental factors operating early in life potently affect developing systems, permanently altering structure and function throughout life. This process with its persistent organizational effects has been called ‘programming’. The brain is a key target for such effects. This review focuses on the effects of adverse early environments, notably exposure to stress or glucocorticoids, upon subsequent adult hypothalamus‐pituitary‐adrenal axis activity, behaviour and cognition. We discuss the effects observed, the proposed underlying molecular and cellular mechanisms and the consequences for pathophysiology. The data suggest that key targets for programming include glucocorticoid receptor gene expression and the corticotrophin‐releasing hormone system. Increasing evidence for analogous processes in humans is also reviewed. Early life programming of neuroendocrine systems and behaviour by stress and exogenous or endogenous glucocorticoids appears to be a fundamental process underpinning common disorders. Approaches to minimize or reverse the consequences of such early life events may have therapeutic importance.