A control system for automated high-resolution preparative gas chromatography is described. On the basis of recorded data from a reference chromatogram, the computer-controlled device automatically corrects for the drift in retention that may occur within a run or during extended operation, and synchronizes fraction collection. Failure to track the reference chromatogram activates an error status and protects the traps for contamination. A specified number of consecutive tracking failures discontinues the repetitive fractionation process. The system can be operated in a simulated mode to facilitate optimization and also includes a control routine to drive auxiliary devices such as an automatic on-column injector or flow switching valves. Cyclic preparative high-resolution fractionation of an essential oil was carried out to evaluate the system. Retention shifts of several seconds were adequately corrected for by the real-time synchronization process, which allowed the precision trapping of closely spaced fractions. Trapping accuracy was also maintained during nearly 800 unattended high-resolution separations of cis- and trans-isopiperitenol. This resulted in the isolation of milligram amounts of the purified isomers and enabled 13C NMR spectra of the components to be recorded.