Inhibition of nuclear factor (NF)-kappaB/Rel can sensitise many tumour cells to death-inducing stimuli, including chemotherapeutic agents, and there are data suggesting that disruption of NF-kappaB may be of therapeutic interest in melanoma. We found that rapamycin sensitised a human melanoma cell line, established from a patient, to the cytolytic effects of doxorubicin. Doxorubicin is a striking NF-kappaB/Rel-inducer, we therefore investigated if rapamycin interfered with the pathway of NF-kappaB/Rel activation, i.e. IkappaBalpha-phosphorylation, -degradation and NF-kappaB/Rel nuclear translocation, and found that the macrolide agent caused a block of IKK kinase activity that was responsible for a reduced nuclear translocation of transcription factors. Western blots for Bcl-2 and c-IAP1 showed increased levels of these anti-apoptotic proteins in cells incubated with doxorubicin, in accordance with NF-kappaB/Rel activation, while rapamycin clearly downmodulated these proteins, in line with its pro-apoptotic ability. The effect of the macrolide on NF-kappa B/Rel induction appeared to be independent of the block in the PI3k/Akt pathway, because it could not be reproduced by the phosphatidyl inositol 3 kinase (PI3k) inhibitor, wortmannin. Recently, the immunophilin, FKBP51, has been shown to be essential for the function of IKK kinase. We found high expression levels of FKBP51 in melanoma cells. Moreover, we confirmed the involvement of this immunophilin in the control of IKK activity. Indeed, IkappaBalpha could not be degraded when FKBP51 was downmodulated by short-interfering RNAs (siRNAs). These findings provide a possible mechanism for the downmodulation of NF-kappaB by rapamycin, since the macrolide agent specifically inhibits FKBP51 isomerase activity. In conclusion, our study demonstrates that rapamycin blocked NF-kappaB/Rel activation independently of PI3k/Akt inhibition suggesting that the macrolide agent could synergise with NF-kappaB-inducing anti-cancer drugs in PTEN-positive tumours.