Adoption of rootstocks is increasing throughout Australian wine regions to address various challenges - both biotic (e.g. pests, diseases) and abiotic (e.g. salinity, drought). As this adoption occurs, it is important to consider how changes in grape composition caused by rootstock variety might affect wine flavour. This is especially relevant for compounds such as methoxypyrazines, which can impart vegetal characters to wine that are difficult to manage post-harvest. Our research has shown that rootstock variety alters the concentration of methoxypyrazines in the rachis of both Cabernet Sauvignon and Shiraz, with concentrations at harvest dependent on region, light exposure, rootstock-mediated vine vigour, and spatial variation in vine vigour. Additionally, the distribution of methoxypyrazines in different rachis components (top rachis, bottom rachis, peduncle and pedicel) were found to be significantly different, with methoxypyrazine concentrations in pedicel at harvest being significantly higher than all other rachis components.