Complex diseases challenge one of the oldest assumptions in medicine: that illness can be reduced to a single cause. Instead, increasing evidence suggests that many pathologies emerge from the collective dynamics of components interacting across molecular, cellular, physiological, behavioral, and ecological scales. Thus, we revisit the fundamental question of what a disease is through the lens of complex systems theory. In particular, we argue that diseases are better understood as emergent dynamical states of living systems that arise from the breakdown, reorganization, or destabilization of regulatory networks. Within this framework, mathematical models can describe health and disease as alternative attractors in a multidimensional state space, and disease onset often reflects critical transitions driven by stress, perturbation, or loss of resilience. Therefore, concepts from nonlinear dynamics, network theory, ecology, and statistical physics (such as bifurcations, hysteresis, phase transitions, and multistability) provide a unifying language to describe phenomena as diverse as patient comorbidity, psychiatric disorders, cancer progression, epidemic spreading, or neurodegeneration. We also discuss how multiscale models can bridge molecular mechanisms with organism-level behavior to reveal universal principles of complex diseases. This perspective implies that the future of medicine may depend on understanding not only the components of biological systems, but also the laws governing their collective organization, which could open new avenues for prediction, prevention, and control.