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Elucidation of the biological effects of the radio frequency (RF) electromagnetic fields has been investigated for decades but it is still not clear weather the observed effects are only due to hyperthermia or non-thermal effects exist as well. In this work, the effect of radio frequency (RF) radiation on protein expression in earthworms E. foetida using two-dimensional protein gel electrophoresis were investigated. Animals were exposed to RF radiation at frequency of 900 MHz and electric field strength of 120 V/m (3.82 mW/cm2) in the Gigahertz Transversal Electromagnetic (GTEM) cell during 2 hours. Obtained data showed an up-regulation of 13 proteins and a down-regulation of 6 proteins in exposed animals. The temperature in earthworm did not raise more than 0.1degC indicating that different mechanisms apart from hyperthermia are involved in the observed effect. In conclusion, an exposure to RF radiation of 900 MHz changed the expression pattern of E. foetida proteins and it seems to be a non-thermal effect.