The possible effects of the electromagnetic fields (EMF) generated by mobile phones on reproductive functions have been discussed in recent years. The aim of this study was to evaluate the effects of EMF emitted from mobile phones on the rat testis morphology and histopathology using stereological techniques. We also investigated cortisol, testosterone, FSH and LH levels. A total of thirty-two (n = 32) male Wistar albino rats were used in this study. Animals were randomly divided into four groups as control (C, n = 8), sham (Sh, n = 8), mobile phone speech (Sp, n = 8) and mobile phone standby (ST by). Morphometric measurements were made with the help of a computer-assisted stereological analysis system. The testis weight and volume were significantly lower in the EMF exposed groups. The mean volume fraction of interstitial tissue was higher, but the volume fraction of tubular tissue was lower in the EMF-exposed groups. The mean tubular and germinal tissue volume, seminiferous tubule diameter and germinal epithelium height were also lower in EMF exposed groups. The cortisol levels in the EMF-exposed groups were significantly higher. In conclusion, the EMF created by mobile phones caused morphologic and histological changes by the affecting germinal epithelium tissue negatively.