The aetio-pathogenetic sequences and the physio-pathological patterns of diabetes, emphysema, cholera, circulatory shock and thrombosis have been analysed with respect to an evolutionary interpretation. The diseases, although reflecting alterations of processes that can always be described in physico-chemical language, occur only at the level of biological systems which reflects the decodification of genomic project: the teleonomic projects that have been developed during evolution. The concepts of evolutionary emergence and of downward causation have been used to discuss the relationship between the molecular events responsible for the initiation of the disease, and the subsequent events responsible for the aetio-pathogenesis, for the systemic disarrangement and for the additional alterations of tissues and cells independent of the initial molecular events. In diabetes the systemic disarrangement, glycosuria and hyperglycemia, reflect the evolutionary emergence of the processes regulating carbohydrate metabolism, whereas the cardiovascular and neurological alterations are effects of the systemic disarrangement by a mechanism of downward causation. The complexity of the aetio-pathogenesis and of the physio-pathological patterns of diseases is due to the generation of information during the evolution of multi-hierarchical entities. The evolutionary epistemology approach is useful to explain the behaviour of complex systems.