John Hughlings Jackson, an English neurologist of the 19th century, proposed that the nervous system was organised as a hierarchical system of three anatomical layers corresponding to a functional hierarchy. The concepts introduced in this description, for the most part in antinomic form, turned out to be fruitful for psychology and psychopathology: psychic evolution/dissolution, simplicity/complexity, organisation/disorganisation, stability/instability, automatism/intentionality, inhibition/disinhibition, brain topology, and Darwinian selection of the most stable states. Henri Ey's adaptation of this architectonic model to the psyche and conscience, which he called organodynamics, required making modifications such as including the intervention of nerve connections between the various brain areas, designated by the term “transanatomical sets”. The most recent synaptic and neuronal models of conscience (J.-P. Changeux, G. Edelman) are presented briefly and include the “selective stabilisation of synapses”. Neurotransmitter anomalies in psychopathy; immunity, inflammatory and synaptic anomalies of certain acute psychoses; and the modifications of synaptic connections after electrical stimulation of the brain are also presented. The convergence of this theoretical and experimental data leads to a discussion of the hypothesis according to which mental diseases might be “synaptic diseases”. Are mental diseases “synaptic diseases” and more specifically, are they “diseases of synaptic connections”? Experimental evidence has shown that synapses are selectively eliminated or stabilized under normal life conditions, in response to stimuli (J.-P. Changeux). The hypothesis that the same is true when the stimuli are pathogenic, seems logical (neurosis, stress), their repetition stabilising dysfunctional circuits. We have just seen that immunity and inflammatory brain anomalies, and anomalies consecutive to electrical stimulation of the brain are also associated with morphological modifications of synapses. In addition, I have proposed elsewhere a “theory of accessory pathways”: Mental pressure, harassment, post-traumatic stress states and ritual actions appear to promote the construction and reorganisation of neuronal networks, which appear to become set under the effect of repetition. Thus, new neuronal networks, and in particular circumventing circuits, could be set up and be stabilised in the form of accessory pathways as with the bundle of Kent in the Wolff-Parkinson-White syndrome. It is supposed that when these accessory pathways become dominant, the patient will lose all critical ability, particularly with respect to himself. Dynamic synaptic modifications (destruction, reconstruction and new connections) could be the basis for such a mechanism, particularly under the effect of pathogenic stimuli, of immune and inflammatory reactions or of neuronal excitation, such as the ones studied above. Psychotherapy and cognitive behavioural therapies are likely to facilitate the regeneration of synaptic connections or the induction of new ones, and their stabilisation. This possibility would support the notion that mental diseases could be “synaptic diseases”, and diseases of synaptic connections in particular. But, this would only the pathophysiological cause, and would leave unexplained the mechanism whereby the mind, as a non material entity, induces biochemical modifications in the neuronal substrate: this could be the case in Janet's “psychasthenia” or with loss of the “life force” (Bergson), which would be “non material causes” of the biochemical, physiological, immunological and inflammatory modifications observed in these mental diseases. Unless we consider, as William James does and as the Changeux and Edelman models suggest, that the mind, and in particular conscience, is only a process resulting from the activity of neuronal circuits, which are damaged in mental disorders. Nicolaï Hartmann's architectonic model, “hierarchical stratification of forms that obey the rule of relative dependence, due to their ontological organisation”, can be presented as follows: the lower layers of psychic structures depend on the upper layers, and the upper layers reciprocally depend on the lower layers. Henri Ey has used this organisation of psychic structures in his concept of “transanatomical sets”. I give these transanatomical entities a dual meaning: they represent on the one hand the organic basis for psychological and psychopathological processes, and on the other hand, the non material psychogenic substance that H. Ey calls “psychic forces” and Henri Bergson “life force”. But, in this article, I wish to develop almost exclusively the notion of transanatomical sets in their relationship to the biological basis for psychopathy, particularly at the cellular and synaptic level.