Healthcare artificial intelligence systems routinely fail when deployed across institutions, with documented performance drops and perpetuation of discriminatory patterns embedded in historical data. This brittleness stems, in part, from learning statistical associations rather than causal mechanisms. Causal graph neural networks address this triple crisis of distribution shift, discrimination, and inscrutability by combining graph-based representations of biomedical data with causal inference principles to learn invariant mechanisms rather than spurious correlations. This Review examines methodological foundations spanning structural causal models, disentangled causal representation learning, and techniques for interventional prediction and counterfactual reasoning on graphs. We analyse applications demonstrating clinical value across psychiatric diagnosis through brain network analysis, cancer subtyping via multi-omics causal integration, continuous physiological monitoring with mechanistic interpretation, and drug recommendation correcting prescription bias. These advances establish foundations for patient-specific Causal Digital Twins, enabling in silico clinical experimentation, with integration of large language models for hypothesis generation and causal graph neural networks for mechanistic validation. Substantial barriers remain, including computational requirements precluding real-time deployment, validation challenges demanding multi-modal evidence triangulation beyond cross-validation, and risks of causal-washing where methods employ causal terminology without rigorous evidentiary support. We propose tiered frameworks distinguishing causally-inspired architectures from causally-validated discoveries and identify critical research priorities making causal rather than purely associational claims.
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