Full thickness skin (FTS), vascularized heterotopic skin-muscle-bone (SMB), and orthotopic hind-limb transplant (CTA) transplants reject at similar time points with no immunosuppression. Under routine continuous immunosuppresion, CTA and SMB can be engrafted; however FTS will still be acutely rejected after a slightly prolonged graft survival time. We hypothesized that FTS, CTA, and SMB would result in distinct patterns of inflammation biomarkers associated with skin rejection in these experimental models. We sought to test this hypothesis and use computational tools to discern underlying factors that explain the unique rejection patterns observed. Materials and methods: FTS, SMB, and CTA were compared. Two samples were taken per group per time point at PODs 1, 3, 5. Brown Norway rats were donors for all groups, and Lewis rats recipients. No immunosuppression was used. Samples included skin and muscle from the allografts (15mm x 10mm excision biopsy), preserved with RNAlaterTM as per manufacturer instructions. LuminexTM 100 IS detected Cytokines with Milliplex Rat 23-plex kit (Millipore), measuring GM-CSF, IL-1a, MCP-1, IL-4, IL-1b, IL-2, IL-6, IL-10, IL-12p70, IL-5, IFN-γ, IL-18, GRO/KC, TNFa, Eotaxin, G-CSF, Leptin, MIP-1a, IL-13, IL-17, IP-10, Rantes, and VEGF. Data were analyzed with MatLabTM (Math Works). Cytokine levels were compared with multivariate ANOVA (MANOVA), and group similarity was measured by mahalanobis distance. Results: The first and second MANOVA canonical variables create significant separation among groups and between tissues (P< 0.01). Mahalanobis distance from FTS to SMB was 3464.8, FTS to CTA was 4001.4, SMB to CTA was 157.4, and Skin to Muscle was 764.9. Conclusion: The results indicate that rejection is associated with distinct, consistent immune/inflammatory signaling patterns for FTS, CTA, and SMB, and these patterns are distinct in skin and muscle. MANOVA coefficients reveal an underlying structure of factors that distinguish rejection in each group. Of these factors, GM-CSF particularly maximizes the differentiation of groups, suggesting that this cytokine plays a pivotal role in the different forms of rejection observed, especially in FTS versus SMB and CTA.