Comprehensive two-dimensional gas chromatography (GC×GC) with a temperature-programmed microfabricated thermal modulator (μTM) is demonstrated. The 0.78 cm(2), 2-stage μTM chip with integrated heaters and a PDMS coated microchannel was placed in thermal contact with a solid-state thermoelectric cooler and mounted on top of a bench scale GC. It was fluidically coupled through heated interconnects to an upstream first-dimension ((1)D) PDMS-coated capillary column and a downstream uncoated capillary or second-dimension ((2)D) PEG-coated capillary. A mixture of n-alkanes C6-C10 was separated isothermally and the full-width-at-half-maximum (fwhm) values of the modulated peaks were assessed as a function of the computer-controlled minimum and maximum stage temperatures of μTM, Tmin and Tmax, respectively. With Tmin and Tmax fixed at -25 and 100°C, respectively, modulated peaks of C6 and C7 had fwhm values<53 ms while the modulated peaks of C10 had a fwhm value of 1.3s, due to inefficient re-mobilization. With Tmin and Tmax fixed at 0 and 210°C, respectively, the fwhm value for the modulated C10 peaks decreased to 67 ms, but C6 and C7 exhibited massive breakthrough. By programming Tmin from -25 to 0°C and Tmax from 100 to 220°C, the C6 and C7 peaks had fwhm values≤50 ms, and the fwhm for C10 peaks remained<95 ms. Using the latter conditions for the GC×GC separation of a sample of unleaded gasoline yielded resolution similar to that reported with a commercial thermal modulator. Replacing the PDMS phase in the μTM with a trigonal-tricationic room temperature ionic liquid eliminated the bleed observed with the PDMS, but also reduced the capacity for several test compounds. Regardless, the demonstrated capability to independently temperature program this low resource μTM enhances its versatility and its promise for use in bench-scale GC×GC systems.