Fumonisins are a family of food-borne mycotoxins with a wide spectrum of toxicological activities, produced by Fusarium verticillioides. Twenty-eight fumonisin analogues have been characterised so far, which can be separated into four main groups, identified as fumonisin A, B, C and P, being fumonisin B the most widely occurring in maize and corn-based food. In this work, major and minor fumonisin analogues produced by F. verticillioides have been determined by the development of a suitable tandem mass spectrometry procedure for target compound identification and quantification. The method has been applied to the determination of the major fumonisins in culture media of F. verticillioides and in mouldy maize. In addition to the main fumonisins produced by F. verticillioides, also secondary compounds such as FB4, FB5, FAs and FCs have been detected in both fungal liquid cultures and contaminated maize samples. The use of this method for quantification of major and minor fumonisins may be useful for an exhaustive evaluation of their occurrence and toxicological relevance in food; moreover, it may be applied for a better definition of the fumonisin biosynthetic pathways in different growing media as well as in maize. Copyright © 2012 John Wiley & Sons, Ltd.