The potential health hazard of exposure to electromagnetic fields (EMF) continues to cause public concern. However, the possibility of biological and health effects of exposure to EMF remains controversial and their biophysical mechanisms are unknown. In the present study, we used Saccharomyces cerevisiae to identify genes responding to extremely low frequency magnetic fields (ELF-MF) and to radiofrequency EMF (RF-EMF) exposures. The yeast cells were exposed for 6 h to either 0.4 mT 50 Hz ELF-MF or 1800 MHz RF-EMF at a specific absorption rate of 4.7 W/kg. Gene expression was analyzed by microarray screening and confirmed using real-time reverse transcription-polymerase chain reaction (RT-PCR). We were unable to confirm microarray-detected changes in three of the ELF-MF responsive candidate genes using RT-PCR (P > 0.05). On the other hand, out of the 40 potential RF-EMF responsive genes, only the expressions of structural maintenance of chromosomes 3 (SMC3) and aquaporin 2 (AQY2 (m)) were confirmed, while three other genes, that is, halotolerance protein 9 (HAL9), yet another kinase 1 (YAK1) and one function-unknown gene (open reading frame: YJL171C), showed opposite changes in expression compared to the microarray data (P < 0.05). In conclusion, the results of this study suggest that the yeast cells did not alter gene expression in response to 50 Hz ELF-MF and that the response to RF-EMF is limited to only a very small number of genes. The possible biological consequences of the gene expression changes induced by RF-EMF await further investigation.