Interest in the early phase of psychotic disorders has risen dramatically in recent years. Neurobiological investigations have focused specifically on identifying brain changes associated with the onset of psychosis. The link between these neurobiological findings and the complex phenomenology of the early psychosis period is not well understood. In this article, we re-cast some of these observations, primarily from neuroimaging studies, in the context of phenomenological models of “the self” and disturbance thereof in psychotic illness. Specifically, we argue that disturbance of the basic or minimal self (“ipseity”), as articulated in phenomenological literature, may be associated with abnormalities in midline cortical structures as observed in neuroimaging studies of pre-onset and early psychotic patients. These findings are discussed with regards to current ideas on the neural basis of self-referential mental activity, including the notion of a putative “default-mode” of brain function, and its relation to distinguishing between self- and other-generated stimuli. Further empirical work examining the relationship between neurobiological and phenomenological variables may be of value in identifying risk markers for psychosis onset.