Considering the current need of low emission fuels for the automotive market and the need of renewable fuels that will emerge in the very next future, Fischer-Tropsch (FT) based technologies should be considered a valid option to accomplish both low emission and renewable fuel production targets. A hydrocracking step is necessary for obtaining high quality fuels from FT wax. lsomerisation is an important reaction that takes place during the hydroconversion process. The amount and the type of the isomers in the produced fuels heavily influence both cold flow properties and cetane number. In this paper the results of a detailed method of analysis which allows the distinction between mono-branched and multi-branched isomers in fuels obtained from an FT wax hydrocracking process, are presented and discussed. In particular the influence of the operating conditions and the wax conversion on the isomer distribution is pointed out. (C) 2010 Elsevier B.V. All rights reserved.