The identification of compounds by using gas chromatography (GC) in samples with significant complexity comprising a range of isomeric species, where characterization is based on peak retention times and mass spectra, generates uncertainty for the analyst. This leads to identification errors. The most reliable way to confirm the identification of each compound is based on authentic standard co-injection, which in several cases is economically prohibitive, and often unachievable in the time available for analysis. Retention index procedures are important tools to minimize misidentification of compounds in conventional chromatography. The introduction of comprehensive two-dimensional GC (GC × GC) for analysis of complex samples was a decisive step to increase the analytical capacity of chromatographic techniques. For many samples, the chromatographic resolution increase leads to quantitative expansion in the number of peaks identified, compared with conventional GC analysis. Notwithstanding this improved resolution, limitations still persist in correct peak identification, which suggests the use of retention indices may assist in supporting component identification in this important technique. In this work, approaches to use of the retention index in GC × GC are discussed, based on an evaluation of the literature in this area. Interpretation of effective chain length data for fatty acid methyl esters in the first and second dimensions is presented.