AbstractThe theory and proof of concept of a new mode of operation for comprehensive two‐dimensional gas chromatography (GC×GC) is presented. In current GC×GC interface designs, the modulation period defines the separation time allowed in the second dimension. In the stop‐flow GC×GC mode, flow in the primary column is periodically stopped for brief periods of time. Consequently, the modulation period for the primary column and the amount of time available for second dimension separation become independent variables. This allows the separations in both the primary and secondary dimensions of the GC×GC system to be carried out under more optimised conditions, allowing extended periods of time for second dimension separations without sacrificing the separation in the primary dimension. This new technique has the potential to offer increased separation power and overall resolution as it is further developed.