The aim of this study was to explore whether, during the course of a 15 days-lasting experiment, a two hours per day and five days per week, 2.45 GHz microwave whole-body irradiation may substantially and therefore provably affect rats’ nocturnal urinary 6-hydroxy-melatonin sulphate (aMT6s) excretion and urinalysis parameters. The average whole-body specific absorption rate (SAR) equalled to 1.25 (± 0.36 SE) W/kg. To collect nocturnal urine samples, animals were held in individual metabolic cages every experimental night from 7:00 PM till 7:00 AM next day. The concentration of aMT6s in rat urine samples was determined by a direct radioimmunoassay. Bilirubin, ketones, and urine protein content have been determined via multiple-use reagent strips. In comparison to the sham-exposed group, no significant changes in body temperature and food or water intake were observed in the exposed group. A decline in aMT6s, determined in the exposed rats, was observed from day 8 to day 11 of the experiment (P < 0.05). The aMT6s level remained consistently low until the end of the experiment, but not significantly lower than the control values. The results of the urine samples biochemical workup failed to reveal any significant differences between the exposed and the control animal groups. The results of this study suggest that, under the above described experimental conditions, repeated 2.45 GHz irradiation could act as a stressor and therefore influence the melatonine balance in rat.