Botryosphaeria dieback is a fungal grapevine trunk disease which represents a threat for viticulture worldwide due to the decreased production of affected plants and their premature death. This dieback is characterized by a typical wood discoloration called "brown stripe". Herein, a proteome comparison of the brown striped wood from Botryosphaeria dieback-affected standing vines cultivar 'Chardonnay', 'Gewurztraminer' and 'Mourvèdre' was performed. The transcript analysis for 15 targeted genes and the quantification of both total phenolics and specific stilbenes were also performed. Several pathogenesis-related proteins and members of the antioxidant system were more abundant in the brown striped wood of the three cultivars, whereas other defense-related proteins were less abundant. Additionally, total phenolics and some specific stilbenes were more accumulated in the brown striped wood. Strongest differences among the cultivars concerned especially proteins of the primary metabolism, which looked to be particularly impaired in the brown striped wood of 'Chardonnay'. Low abundance of some proteins involved in defense response probably contributes to make global response insufficient to avoid the symptom development. The differential susceptibility of the three grapevine cultivars could be linked to the diverse expression of various proteins involved in defense response, stress tolerance and metabolism.