Volatile compounds are together with sugars and organic acids the main determinants of tomato fruit flavour and are therefore important for consumer acceptance. Consequently, in the last years many studies have been performed using different volatile analytical techniques on a large diversity of tomato fruits, aimed mainly at detecting the compounds affecting flavour or at the identification of QTLs and key genes involved in fruit volatile contents. The comparison of three of the analytical methods most commonly applied (headspace, solid phase microextraction, adsorption on Tenax followed by thermal desorption) revealed not only differences in sensitivity, but also dramatic variations in the volatile profile obtained by each of these techniques. The volatile profile was also largely influenced by the way samples were processed before analysis. Four widely used sample processing methods were compared (whole tomato, sliced fruit and two different types of fruit paste), each one producing a characteristic volatile pattern. Therefore, great care should be taken when comparing results available from the literature obtained by means of different methods, or when using the volatile levels obtained in an experiment to predict their influence on tomato flavor or consumer preference, or to assess the success of breeding programs.