Repetitive DNA (RE-DNA) was long thought to be silent and inert; only recent research has shown that it can be transcribed and that transcription alteration can be induced by environmental stress conditions, causing human pathological effects. The aim of this study was to determine whether exposure to radiofrequency electromagnetic fields (RF-EMF) could affect the transcription of RE-DNA. To this purpose, three different human cell lines (HeLa, BE(2)C and SH-SY5Y) were exposed to 900 MHz GSM-modulated RF-EMF at specific absorption rate of 1 W/kg or to sham. After exposure, mRNA levels of RE-DNA were evaluated through quantitative real-time PCR. The following RE-DNA types were investigated: Long Interspersed nucleotide Element 1, DNA alpha satellite and Human Endogenous Retroviruses-like sequences. When comparing cells exposed to RF-EMF versus control samples, different results were found for the three cell lines evaluated, indicating that RF-EMF exposure can significantly affect RE-DNA transcription and that the effects strongly depend on the cellular context and the tissue type. Further studies are needed to elucidate which molecular mechanisms could be involved.