Myogenin and the fetal type acetylcholine receptor (AChR) subunits are specific immunohistochemical markers for the diagnosis of rhabdomyosarcomas. In spite of light microscopy and immunohistochemistry, the diagnosis of doubtful cases and small biopsies of rhabdomyosarcomas remains a challenge. Therefore, a PCR-based highly sensitive approach, would be a valuable diagnostic adjunct and should be free from the risk of contamination of the tumor sample with normal tissue. We studied the transcription of myogenin and fetal type AChR in rhabdomyosarcomas, other childhood and adult tumors and normal tissues. In all embryonal and alveolar rahbdomyosarcomas transcripts of both myogenin and fetal type AChR could be detected. The detection of myogenin mRNA however was not specific for rhabdomyosarcomas but occurred in normal muscle and the majority of other normal tissues and childhood tumors. In contrast the transcription of fetal type AChR, which is defined by an alpha subunit AChR/gamma subunit AChR ratio < 1 was encountered only in rhabdomyosarcomas and denervated muscle. Therefore we suggest, that mRNA of the fetal type AChR but not myogenin is a highly specific and sensitive target for the PCR-based diagnosis of rhabdomyosarcomas.