Background Current methods to repair ablation-type peripheral nerve injuries (PNIs) using peripheral nerve allografts (PNAs) often result in poor functional recovery due to immunological rejection as well as slow and inaccurate outgrowth of regenerating axonal sprouts. In contrast, ablation-type PNIs repaired by PNAs using a multistep protocol, in which one step uses the membrane fusogen polyethylene glycol (PEG), permanently restore sciatic-mediated behaviors within weeks. Axons and cells within the PNA remain viable, even though outbred host and donor tissues are neither immunosuppressed nor tissue matched. PEG-fused PNAs exhibit significantly reduced T cell and macrophage infiltration, apoptosis, and expression of major histocompatibility complex I/II. In this study, we analyzed the coding transcriptome of PEG-fused PNAs to examine possible mechanisms underlying immunosuppression. Methods Ablation-type sciatic PNIs in adult Sprague Dawley rats were repaired using PNAs and a PEG-fusion protocol combined with neurorrhaphy. Electrophysiological and behavioral tests confirmed successful PEG-fusion of PNAs. RNA sequencing analyzed differential expression profiles of protein-coding genes between PEG-fused PNAs and Negative Control PNAs (not treated with PEG) at 14d PO, along with Unoperated Control nerves. Sequencing results were validated by Quantitative Reverse Transcription PCR (RT-qPCR). Results PEG-fused PNAs display significant downregulation of many gene transcripts associated with innate and adaptive allorejection responses. Schwann cell-associated transcripts are often upregulated, and cellular processes such as extracellular matrix remodeling, cell and tissue development are particularly enriched. Transcripts encoding several potentially immunosuppressive proteins (e.g. Thrombospondins 1 and 2) are also upregulated in PEG-fused PNAs. Conclusions This study is the first to characterize the coding transcriptome of PEG-fused PNAs, and identifies possible links between alterations of the extracellular matrix and suppression of the allorejection response. The results establish a molecular-basis to begin to understand mechanisms underlying PEG-mediated immunosuppression.