Esca complex disease seriously affects vine yield and longevity. Because of the time delay between wood infection by fungi and symptom expression, current disease diagnosis relies on destructive sampling of the wood, usually a difficult and costly procedure. The goal of this study was to identify metabolites that could be used as biomarkers for developing a noninvasive biochemical method for early diagnosis of esca complex disease. A Q-Exactive Hybrid Quadrupole-Orbitrap high resolution/accurate mass spectrometric-based platform was used to assess the lipidomic profile of healthy leaves from healthy vines, asymptomatic leaves from wood-affected vines, and symptomatic leaves with two different degrees of severity. Biochemicals were separated on ultrahigh performance liquid chromatography and gas chromatography. A total of 208 compounds were detected, including fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, prenol lipids, sterol lipids, hormones, carotenoids, chlorophylls, and metabolites of the carnitine and choline metabolisms. Biomarkers of symptom emergence were identified by different classification methods, including volcano plots, hierarchical clustering, principal component analysis, pathway mapping and rich factor analysis. Of all the biochemical classes, the galactolipid class (glycerophospholipids) was the only variable that explained differences among experimental groups. Indeed, the levels of 13 galactolipids increased in leaves of asymptomatic vines, and progressively decreased with the appearance of foliar symptoms. A positive correlation between the level of leaf necrosis and levels of galactolipids was found, suggesting a role for galactolipids in the etiopathogenesis of esca complex disease. Such information could be used for identification of esca-affected vines without the need to rely upon symptomatic descriptors.