Comprehensive, two-dimensional gas chromatography (GC x GC) chromatogram's typically exhibit run-to-run retention time variability. Chromatogram alignment is often a desirable step prior to further analysis of the data, for example, in studies of environmental forensics or weathering of complex mixtures. We present a new algorithm for aligning whole GC x GC chromatograms. This technique is based on alignment points that have locations indicated by the user both in a target chromatogram and in a reference chromatogram. We applied the algorithm to two sets of samples. First, we aligned the chromatograms of twelve. compositionally distinct oil spill samples, all analyzed using the same instrument parameters. Second, we applied the algorithm to two compositionally distinct wastewater extracts analyzed using two different instrument temperature programs, thus involving larger retention time shifts than the first sample Set: For both sample sets, the new algorithm performed favorably compared to two Other available alignment algorithms: that of Pierce, K. M.; Wood; Lianna F.; Wright, B. W.; Synovec, R. E Anal Chem. 2005, 77, 7735-7743 and 2-D COW from Zhang, D.; Huang, X; Regnier, P. E; Zhang, M. Anal Chem. 2008, 80, 2664-2671. The new algorithm achieves the best matches of retention times for test analytes, avoids some artifacts which result from the other alignment algorithms, and incurs the least modification of quantitative signal information.