An experimental investigation was carried out with the aim to investigate on the isomerisation of 1,2-diacylglycerols to 1,3-diacylglycerols as a function of the storage conditions, as well as to identify indices useful to evaluate the freshness of the oils. Two oils derived from two different cultivars (Coratina and Ogliarola barese) were stored for two years as follows: in bottles at dark; in clear glass bottles at light; in green glass bottles at light; in bottles at dark, the latter subjected to repeated opening and samplings to simulate domestic use. The obtained results evinced that during the storage period a significant increase in the 1,3-isomers was observed due to an isomerisation from the 1,2 to the 1,3 isomeric form, consequently the 1,3/1,2 ratio increased in both oils. The covariance analysis of the data showed that the isomerisation of diacylglycerols, taking place during time, was affected by the type of oil, probably due to the different initial hydrolysis level, but was not affected by the storage conditions. Among the parameters considered, the total diacylglycerols/1,3-diacylglycerols ratio could be used as freshness index of extra virgin olive oil, since it is not affected by either oil or storage conditions.