A two-dimensional retention index system for fatty acid methyl esters (2D-FARI) is proposed. The system is based on the application of different temperature and pressure programs on a single capillary column. A calibration sample is analysed and the retention data is calibrated against a set of reference 2D-FARI values. The calibration models are then applied to predict the 2D-FARI values for compounds that are not present in the calibration sample. The two dimensions in the retention index system lead to increased selectivity and a reduced risk of retention index overlap between different compounds. The 2D-FARI system is also more robust towards differences in stationary phase properties than ordinary retention indices and is therefore convenient for comparison of retention data acquired on different columns, or at different times at the same column.