The aim of the work was to assess the parameters of the heart rate variability of the user by the interfaces of the brain-computer, oculographic, respiratory, myographic, depending on the SNV in the genes that are somehow related to the functioning of the autonomic nervous system. Heart rate variability is an indicator of the cardiovascular system and a number of mechanisms regulating the whole organism, which can be used as one of the markers of the state of a human operator. The paper analyzes the association of point mutations of the HTR2A, APOE and TPH2 genes with HRV indices when users master a number of human-computer interfaces: brain-computer, oculographic, myographic and respiratory. The brain-computer interface is implemented on stable (well-established) visual evoked potentials; oculographic interface provided a set of text by eye movement, myographic provided the same task as the two above interfaces, due to changes in the user’s muscular activity; respiratory interface — due to changes in breathing. It has been shown that the SNV of the HTR2A and TPH2 genes involved in serotonin metabolism are associated with HRV indices in the development of neurocomputer interfaces. The SNV rs6313 HTR2A C allele carriers are characterized by higher rates of tonic effects on HRV when working with the oculographic interface, which is probably associated with an increase in serotonin receptor expression, which is involved in the vegetative regulation of heart rhythm. The genotype T / T SNV rs4290270 of the TPH2 gene is associated with a large spread of cardiointervals. This is probably due to an increase in the expression of the TPH2 gene, which catalyzes the limiting step of serotonin synthesis.