Recent studies indicate that exposure to extremely low frequency magnetic fields (ELF MFs) influences human electroencephalographic (EEG) alpha activity and pain perception. In the present study we analyse the effect on electrical EEG activity in the alpha band (8–13 Hz) and on nociception in 40 healthy male volunteers after 90-min exposure of the head to 50 Hz ELF MFs at a flux density of 40 or 80 T in a double-blind randomized sham-controlled study. Since cardiovascular regulation is functionally related to pain modulation, we also measured blood pressure (BP) and heart rate (HR) during treatment. Alpha activity after 80 T magnetic treatment almost doubled compared to sham treatment. Pain threshold after 40 T magnetic treatment was significantly lower than after sham treatment. No effects were found for BP and HR. We suggest that these results may be explained by a modulation of sensory gating processes through the opioidergic system, that in turn is influenced by magnetic exposure.