Introduction Cognitive deficits are basic in schizophrenia. It's important to research nascent defect in schizophrenia with early onset. The decision of this problem requires multidisciplinary approach (neuropsychological, psycho-diagnostic, clinical). Methods Children and adolescents with emerging defect of endogenous mental disorders (18 persons, 8 girls, mean age 11.3, diagnoses: F21, F20.8 and F2x.x) were compared in IQ (WISC) and neuropsychological status (battery of Luria tests). All children were tested at hospital and got psychopharmacologic treatment. Evaluation parameters IQ (Wechsler scale) Verbal IQ score, a non-verbal IQ score, the general intellectual index(IQ). All sorts of IQ were divided into high, medium and low ones. Neuropsychological assessment parameters: dysfunction of subcortical structures, aborted hemispheric interaction, functional aborted (dysfunction) of the cortical divisions. Three-point scale corresponding to the severity of dysfunction was used in the study. Objectives analysis of options relation of mental deficiency (IQ) and neuropsychological status in nascent defect in children and adolescents with of endogenous mental disorders. Results Clustering neuropsychological assessment identified two clusters, the differences between them were related to the degree of neuropsychological deficiency. First - more expressed dysfunction, the second - less severe. Clustering IQ and neuropsychological assessment also identified two clusters. The first included patients with relatively low IQ and enough of neuropsychological deficit, and the second - with the opposite characteristics. Conclusions Complex psycho-diagnostic and neuropsychological assessment of cognitive status children and adolescents with emerging defect of endogenous mental disorders let's talk about a high degree of conformity intellectual indicators IQ and neuropsychological deficits in these patients.