According to a linguistic tradition here termed ‘Cartesian’, language is relegated to an expressive system considered to provide the means to encode or communicate an independently constituted thought process. An alternative vision here termed ‘un-Cartesian’ regards language as an organizational principle of human-specific thought, with the implication that thought of the same type would not become available to a cognitive system without language and that clinical thought disturbances implicate language dysfunction. I here explore the latter view in the context of intra-species variation of the human cognitive type: cognitive disorders that, as in the case of autism and schizophrenia, come with language-related clinical symptoms. If language is the configurator of human-specific thought, cognitive and linguistic phenotypes should illuminate one another. I specifically review evidence for impairment in one universal linguistic function, namely reference. Linguistic meaning is referential meaning: we cannot utter sentences without referring to persons, objects, and events, based on lexicalized concepts that provide descriptions of these referents. Reference in this sense takes a number of human-specific forms, from generic to specific, deictic and personal ones, which empirically co-vary with forms of grammatical organization. As reference in some of these forms proves to be highly vulnerable across major mental disorders, grammar is thereby linked to forms of thought and selfhood critical to normal cognitive functioning. In this way clinical linguistic and cognitive diversity provides an important new window into the foundational question of the thought-language relationship and the cognitive significance of grammar.