Objectives: The aim of this paper is to test the influence of long-term application of the low-frequency magnetic fields in magnetotherapy and magnetostimulation on cortisol secretion in men. Materials and Methods: Patients were divided into three groups: 16 men underwent magnetotherapy and 20 men (divided into two groups) underwent magnetostimulation. Magnetotherapy -2 mT induction, 40 Hz, bipolar square wave, was applied for 20 min to lumbar area. Magnetostimulation (Viofor Jaroszyk, Paluszak, Sieroń (JPS) system, M2P2 program) was applied to 10 patients for 12 min each day. The third group (10 patients) underwent magnetostimulation (Viofor JPS system, M3P3) for 12 min each day using a different machine. All groups had 15 rounds of applications at approximately 10:00 a.m. with intermissions on the weekends. Blood serum was taken four times in a 24-hour period, before applications, the day after applications and a month later. Chemiluminescence micromethod was used to indicate hormone concentrations. Data was statistically analyzed with the analysis of variance (ANOVA) method. Results: The statistically significant gains in the circadian cortisol profile at 4:00 p.m., before and after application, were observed as a decrease in concentration during magnetotherapy. In magnetostimulation, with the M2P2 program, a significant increase in the cortisol concentration was observed in circadian profile at 12:00 p.m. one month after the last application. After magnetostimulation with the M3P3 program, a significant increase in concentration at 6:00 a.m. and a decrease in concentration at 12:00 p.m. were observed one month later. Statistically significant difference was demonstrated in the participants after the application of magnetotherapy and magnetostimulation with M3P3 program compared to the men submitted to magnetostimulation, with M2P2 program, at 4:00 p.m. after 15 applications. Conclusions: Biological hysteresis one month after magnetostimulation suggests long-term influence on the hypothalamohypophysial axis. The circadian curves of cortisol secretion a day after magnetotherapy and magnetostimulation with M3P3 program compared to magnetostimulation with M2P2 progam differs nearly by 100%, which proves that they show varied influence on cortisol secretion in men. All changes in the hormone concentration did not exceed the physiological standards of cortisol secretion, which suggests a regulating influence of magnetic fields on cortisol concentration rather than a strong stressogenic impact of magnetostimulation.