Wine is an extremely complex beverage that contains a multitude of volatile and non-volatile compounds. This study investiged the effect of vineyard site and grapevine clone on the volatile profiles of commercially produced Pinot Noir wines from Central Otago, New Zealand. Volatile metabolites in Pinot Noir wines produced from five grapevine clones grown on six vineyard sites in close proximity, over two consecutive vintages were surveyed using gas-chromatography mass spectrometry (GC-MS). The raw GC-MS data was processed using parallel factor analysis (PARAFAC2) and final metabolite data was analysed by principal component analysis (PCA). Winemaking conditions, vintage and barrel maturation were found to be the most dominant factors. The effects of vineyard site and clone were mostly vintage dependent. Although four compounds including β-citronellol, homovanillyl alcohol, N(3-methylbutyl)acetamide and N(2-phenylethyl) acetamide discriminated the vineyard sites independant of vintage, Pinot Noir wines from different clones were only partially discriminated by PCA and marker compound selection remained challenging.