The expression of genes encoding serotonin receptors and serotonin transporter in emotiogenic structures of rat brain was shown to change after chronic stress with ultrasonic waves of varying frequencies. A QPCR-RT study revealed the increased expression of genes for SERT and 5-HT1B receptor and decreased expression of the 5-HT2A receptor in the prefrontal cortex of rats after chronic exposure to ultrasonic waves of varying frequencies. Gene expression was increased for SERT, but decreased for 5-HT1B, 5-HT2A, and 5-HT2B receptors in the midbrain of animals. The hippocampus was characterized by an increased expression of genes encoding SERT and 5-HT1A, 5-HT2A, and 5-HT2B receptors. Our results indicate that the exposure to this type of stress is followed by dysregulation in the serotoninergic system of the brain.