Among fungal grapevine trunk diseases, esca proper poses a significant threat for viticulture. Apoplexy, mainly occurring on grapevines affected by esca proper, is also a threat. To verify if different responses are activated in the woody tissues of apoplectic (A) and esca proper-affected (E) vines, two-dimensional gel electrophoresis coupled to mass spectrometry analysis was used to examine changes in the trunk wood of E and A field-grown plants. Asymptomatic and black streaked trunk (BST) wood from A and E plants were compared to asymptomatic and BST wood of control plants. Twenty-seven differentially expressed protein spots were identified. For eleven targeted proteins, expression of the relative transcripts was also monitored by qRT-PCR. Hierarchical tree clustering revealed differences in the distribution of spots containing carbohydrate metabolism proteins and heat shock proteins between asymptomatic- and BST-wood of grapevine, irrespective of the type of plant examined (control or diseased grapevines). Asymptomatic wood was mainly characterized by down-expression of proteins involved in cell growth and defense responses. The proteome of BST wood, characterized by extensive presence of grapevine trunk disease agents, revealed over-expression of proteins involved in defense. There was no evidence of strong different response in the trunk wood of apoplectic and esca proper affected plants. This could mean that, despite the different feature of these external crown symptoms, grapevine responses at trunk wood level is very similar in both cases. This plant response might therefore either simply be due to the fact that plants can react in the same way to different stresses, or that apoplexy represents a different effect provoked by the same cause or causal agent(s).