Serotonin (5-hydroxytryptamine, 5-HT) is an important modulatory neurotransmitter and functions as a key neurodevelopmental signal in the mammalian brain. 5-HT plays a prominent role in regulating various types of psychological processes and functions, including mood and emotion, particularly anxiety, but also in regulating social behavior. Consequently, the 5-HT system is implicated in various neuropsychiatric disorders, such as anxiety disorders and depression or autism spectrum disorders (ASD), with selective 5-HT reuptake inhibitors being the frontline medication. Mice and rats perceive and emit ultrasonic vocalizations (USV). It is widely believed that the various distinct USV types reflect the animal's affective state, such as anxiety or pleasure. Furthermore, they serve communicative functions, for instance, as alarm calls or social contact calls. Manipulations targeting the 5-HT system alter affective ultrasonic communication in rodents throughout life, probably because of its important role in regulating anxiety and social behavior. Ample evidence indicates the involvement of the 5-HT system in modulating isolation-induced USV in pups. Later in life, the 5-HT system plays a strong modulatory role in the emission of aversive 22-kHz USV in rats. So far, little is known about the role of 5-HT in the production of interaction-induced USV in mice and appetitive 50-kHz USV in rats, although recent findings also suggest a modulatory effect of the 5-HT system. Assessment of rodent USV is a valuable method to investigate mood and emotion, and to enhance our understanding of, and develop novel pharmacological therapies for neuropsychiatric disorders, such as anxiety disorders and depression or ASD.