Grafting plants uses intrinsic healing processes to join two different plants together to create one functional organism. To further our understanding of the molecular changes occurring during graft union formation in grapevine, we characterized the metabolome and transcriptome of intact and wounded cuttings (with and without buds to represent scions and rootstocks respectively), and homo- and heterografts at 0 and 14 days after wounding/grafting. As over-wintering, dormant plant material was grafted, we also characterized the gene expression changes in the wood during bud burst and spring activation of growth. We observed an asymmetrical pattern of gene expression between above and below the graft interface, auxin and sugar related genes were up-regulated above the graft interface, while genes involved in stress responses were up-regulated below the graft interface.