The research into the effects of low frequency magnetic fields on living organisms has focused so far on the fields produced by power lines, industry and mobile telecommunication. Although they may influence procreation and teratogenesis, the pulsating magnetic fields that are used in physical therapy have not been sufficiently studied with regard to their impact on the endocrine system Aim: The aim of the study was to test the influence of magnetic fields applied in long-term magnetotherapy and magnetostimulation (as in physiotherapy) on the secretion of pituitary (FSH, LH, prolactin) and sex (testosterone, estradiol) hormones in men. Methods: In the research, the patients were divided into three groups: the magnetotherapy group of 16 men and the magnetostimulation group of 20 men (in two groups). Magnetotherapy in the form of magnetic field induction, 2.9 mT, 40 Hz frequency, a bipolar square wave generated by Magnetronic MF-10, was applied for 20 minutes to the lumbar area in patients suffering from chronic low back pain. Magnetostimulation (Viofor JPS system, M2P2 program with a mat as the applicator) was applied for 12 minutes a day in 10 patients treated for the same complaint. The third group of 10 patients was also treated with magnetostimulation (Viofor JPS system, M3P3 program with a mat as the applicator) for 12 minutes a day. All the groups went through 15 sessions that took place at about 10.00 am, one application a day with breaks for weekends. The chemiluminescence micromethod was used to estimate the concentration of hormones (FSH, LH, prolactin, testosterone in ng/dl and estradiol in pg/dl). The data were statistically analyzed with the use of the ANOVA method. Results: Magnetotherapy did not affect hormone secretion in patients treated for low back pain. Magnetostimulation affects the concentrations of prolactin, estradiol and testosterone. After the application of M2P2 program, a significant reduction in the concentration of prolactin, as compared to the basal values, was observed a month after the applications. A significant decrease in the concentration of estradiol was observed immediately after the end of the applications and a month later. Furthermore, the application of M3P3 program produced a significant increase in the concentration of estradiol after 15 sessions, and then a decrease in the concentration was noted a month after the applications. A drop in the concentration of testosterone was observed immediately after the end of the treatment and a month later. Conclusions: The results indicate a possible effect of the magnetic fields used in magnetostimulation on the secretion of prolactin, estradiol and testosterone as they reduce the secretion of these hormones. Both the magnetostimulation programs have a similar effect on the concentration of estradiol. The influence of the magnetic fields used in physiotherapy on the secretion of these hormones requires further research on a larger number of participants, including women.