Aim: Wine quality is influenced by the nitrogen nutrition of grapevines in the vineyard. A deficiency of this nutrient will affect grape quality, decrease yeast available nitrogen (YAN) and influence alcoholic fermentation. Chasselas wines from nitrogen-deficient grapes (YAN < 140 mg N/L) are systematically more astringent and bitter and less fruity than those from grapes with higher YAN content (Spring et al., 2014). The aim of this study was to identify chemical markers in wine linked to nitrogen deficiencies in the vineyard. Methods and results: Wine samples produced from grapes growing in nitrogen-deficient vineyards with nitrogen treatment (HN) and without it (LN) were used over four consecutive years (2006–2009). They were all analysed at the same time (2012) with electronic-nose, GC-MS and UHPLC-TOFMS techniques. A metabolomics approach was used for a comprehensive survey of volatile and nonvolatile compounds in order to identify markers related to nitrogen nutrition. Volatile markers with alcohol and ester functions and nitrogen-containing compounds were found and tentatively identified by GC-MS. Additionally, 16 nonvolatile markers were putatively identified by UHPLCTOFMS, including compounds from diverse chemical classes, namely, amino acids, vitamins, hormones, organic acids, phenolic compounds and polysaccharides. Conclusion: The nitrogen nutrition of grapevines has a clear but complex effect on the chemical composition of wine. Several markers were tentatively identified and their role in wine composition discussed according to the actual knowledge reported in the literature. Significance of the study: This study is an important starting point for selecting the most relevant chemical markers in wine, and for determining whether organoleptic problems are related to nitrogen nutrition deficiency in the vineyard and changes in vineyard management are needed.