Objectives: It is known that professional occupation affects the heart rate variability (HRV). However, most studies have not taken into account seasonal features of the HRV. The aim of this study has been to evaluate the HRV differences in winter and in summer in the case of the Ministry of the Russian Federation for Civil Defense, Emergencies and Elimination of Consequences of Natural Disasters (EMERCOM) workers and scientific workers from the Komi Science Center of the Ural Branch of the Russian Academy of Sciences. Material and Methods: The short-term HRV was examined for 13 EMERCOM workers and 13 scientific workers. The data was collected in winter (December) and summer (July) for the same groups of workers. The time domain and frequency domain HRV analyses were performed. The EMERCOM workers had more contact with the external environment than the scientific workers. Results: The two-way analysis of variance with repeated observations on a single factor has shown that “Season” and interaction of two factors “Season” and “Profession” significantly influenced the HRV among volunteers. The “Profession” factor did not influence the HRV parameters (except for the heart rate in winter, p = 0.042). Seasonal changes in the HRV parameters were not significant in the case of scientific workers. In contrast, the EMERCOM workers showed significantly decreased parameters of parasympathetic activity (the root-mean-square of successive differences in RR intervals, percentage of consecutive RR intervals differing by > 50 ms and the relative value high frequency power, p = 0.001, p = 0.014 and p = 0.009, respectively) and increased parameters of sympathetic activity (the stress index and ratio of low-frequency power to high-frequency power, p = 0.012 and p = 0.006, respectively) in winter as compared to summer. Conclusions: The results of our study indicate that, unlike the scientific workers, the EMERCOM workers showed significant changes in the HRV in contrasting seasons (winter and summer). A season of a year should be considered when assessing the HRV among workers of various professions. Int J Occup Med Environ Health 2016;29(5):793–800