<p>Fatigue is a severely disabling symptom that can substantially impair quality of life and employment prospects, and has serious socioeconomic consequences. Different individual and disease-related variables interact to generate this complex symptom, leading to clinical heterogeneity. We currently lack a common understanding and definition of fatigue and its origins, thereby impeding professional exchange among disciplines regarding diagnosis and underlying pathophysiology. To aid the development of a common language that encapsulates the heterogeneity of fatigue, we propose a taxonomy consisting of neurogenic, myogenic and systemic clusters. Each cluster comprises the same five distinct concepts and their phenotypic expression. The interplay between multifactorial pathophysiological mechanisms might vary between diseases and over time, and additional factors such as comorbidities can modulate fatigue. Understanding this complexity is essential to improve both the diagnostic process and the development of targeted therapeutic interventions. In this Review, we compare the clinical and pathophysiological characteristics of a range of neurological and non-neurological diseases within predefined clusters of fatigue origin. We propose an integrative model for fatigue of different origin and over time based on the interplay of genetics and epigenetics, immunological changes, structural and functional brain abnormalities, and behavioural alterations. Large research consortia will be required to tackle the methodological shortcomings that currently hamper our understanding of fatigue and to initiate large longitudinal cohort studies with multidimensional readouts to further explore and address this burdensome symptom.</p>