Islet-grafts can contribute to their own destruction via the elaboration of proinflammatory genes, many of which are transcriptionally regulated by NF-κB. Thus NF-κB constitutes an enticing gene therapy candidate to improve the success of islet transplantation. To test this hypothesis in vivo, we blocked NF-κB in BALB/c (H-2d) to C57/BL6 (H-2b) mouse islet allografts by genetically-engineering islets to express the NF-κB super-repressor, IκBα. Here we show by microarray and RTqPCR that islets exhibit an intrinsic early-immediate pro-inflammatory response; with the most highly up-regulated proinflammatory genes comprising the chemokines Cxcl1, Cxcl2, Cxcl10 and Ccl2; the cytokines Tnfα and Il6; and the adhesion molecule Icam1. Overexpression of IκBα inhibited the expression of these genes by 50-95 % in islets and MIN6 β-cells in vitro, by inhibiting NF-κB-dependent gene transcription. Histological and RTqPCR analysis at post-operative day (POD) 10 revealed that IκBα transduced islet allografts exhibited improved islet architecture and strong insulin-labelling with decreased Ccl2 and Il6 mRNA levels compared to GFP-transduced control grafts. Despite these protective effects, NF-κB blocked islet allografts were promptly rejected in our MHC mismatched mouse model. However, IκBα expressing grafts did harbour localized 'pockets' of Foxp3+ mononuclear cells not evident in control grafts. This result suggested to us that the effect of NF-κB blockade might synergize with regulatory T-cell sparing Rapamycin. Indeed, combining intragraft IκBα expression with low-dose Rapamycin increased the mean survival time of islet allografts from 20 to 81 days; with 20 % of grafts surviving for greater than 100 days. In conclusion, Rapamycin unmasks the protective potential of intragraft NF-κB blockade, which can, in some cases, permit permanent allograft survival without continuous systemic immunosuppression.