Abstract: Background: The Autonomic Nervous System (ANS) is involved in the response to various emotional stimuli like anxiety, stress, and the sense of wellbeing. As a control system the ANS plays a variety of roles in humans, including regulation of the cardiac function, which can be studied by analyzing heart rate variability (HRV). HRV coherence has been associated with a sense of wellbeing, along with enhanced cognitive, social, and physical performance. Extremely low frequency electromagnetic fields (ELF-EMF) are used in a variety of clinical areas, however very little is known to date about the functional mechanisms involved in vivo. An interaction with the ANS is one of the possible ways in which the effects of ELF-EMF therapy are modulated in living systems. In this single-blind study the effects on the ANS of 5 different electromagnetic configurations were analysed by measuring the HRV using a HeartMath® EmWave® Pro device. Materials and methods: 46 healthy subjects of 20 to 30 years in age were recruited and divided into two groups (treatment group μ and control group λ). After measuring the baseline HRV coherence state (ω) the subjects in group μ were assessed during administration of 5 different ELF-EMF configurations from a SEQEX® device, all at the same intensity of 20 μT (the name attributed to the configuration is in brackets) for a duration of 3 min. each: 1-3 Hz (δ), 4-8 Hz (θ), 9-13 Hz (α), 15-29 Hz (β), and 31-56 Hz (γ). The subjects in group λ were measured in the same way and the same number of times. Results: The initial coherence values ω were comparable between the two groups (μ: 36%, λ: 36.39%). Under the 1-3 Hz (δ) and 15-29 Hz (β) treatment configurations, group μ had an average HRV coherence of 46.26% and 47.26% respectively, while group λ had 38.13% and 37.39% respectively, representing a significant increase in HRV coherence under treatment (pδ = 0.035 and pβ = 0.046). Conclusions: The ANS appears to be sensitive in a frequency dependent manner to treatment with ELF-EMF. This is very important, if confirmed in further studies, not only for better understanding the mechanism of action of ELF-EMF on complex biological systems, but more importantly for therapeutic purposes under different levels of psychopathological discomfort like stress and anxiety, as well as for modulating perceived pain and organ dysregulation.