Objective. To evaluate the state of complement system (CS) activity in children with autistic spectrum disorders (ASD) and children with schizophrenia on the basis of development and implementation of a new method of CS determination. Material and methods. A study included 249 patients, aged from 3 to 14 years. The control group consisted of 279 age-matched children. The authors developed a method for integral evaluation of CS activity based on the changes in the death of free swimming ciliata Tetrahymena pyriformis measured with the apparatus BioLat (Moscow, Russia). The integral CS activity (T50) was estimated as the time of death of 50% of ciliata in the blood serum (serum concentration was 5%). Results and conclusion. A comparative analysis of CS activity showed statistical differences in median T50 values between patients and controls (p<0.005). Based on CS activity levels, three groups of patients were determined: 1) with the levels lower than the lowest value of the control group (n=112 (39%)); 2) higher than the highest level of the control group (n=103 (36%)); intermittent between low and high values of the control group (n=72 (25%)). Significant differences in T50 between the psychotic autism group and children schizophrenia group were identified (p<0.005). The CS activity was lower in patients with ASD compared to children with schizophrenia.