The interconversion of E and Z isomers of acetaldoxime 1 and butyraldoxime 2 have been investigated by comprehensive two-dimensional dynamic gas chromatography (DGCxDGC) and computer simulation. Time-resolved cryogenic modulation is capable of revealing the precise isomeric ratio as a fine structure under the dynamic elution profile, which is characterized in one-dimensional experiments by a plateau formation or peak coalescence caused by interconversion of the isomers during the separation process. The chromatographic theoretical plate model has been extended for the computer simulation of comprehensive two-dimensional dynamic chromatographic experiments. A novel program, ChromWin 2D, based on the new algorithm has been developed for computer simulation to evaluate and predict the elution profiles of DGCxDGC experiments. ChromWin 2D allows the determination of rate constants and barriers of isomerization, epimerization, and enantiomerization processes occurring during chromatographic separations. The Eyring activation parameters of the E/Z and Z/E isomerization barriers in the presence of the stationary phase BP21 (poly(ethylene glycol) terephthalate terminated) were determined by temperature-dependent experiments between 80 and 90 °C for 1 and 70 and 130 °C for 2. The thermodynamic Gibbs free energy of the E/Z equilibrium of the isomers has been determined from the time-resolved chromatograms by cryogenic modulation. The method described here constitutes a new and important tool for the determination of isomerization barriers, which are of great interest, for example, for the quantitative determination of derivatized aldehydes, such as dinitrophenylhydrazine derivatives, in trace analysis.