Temperature programming of gas chromatography (GC) separation columns accelerates the elution rate of chemical species through the column, increasing the speed of analysis, and hence making it a favorable technique to speedup separations in microfabricated GCs (micro-GC). Temperature-programmed separations would be preferred in an all-silicon micro-column compared to a silicon-Pyrex® micro-column given that the thermal conductivity and diffusivity of silicon is 2 orders of magnitude higher than Pyrex®. This paper demonstrates how to fabricate all-silicon micro-columns that can withstand the temperature cycling required for temperature-programmed separations. The columns were sealed using a novel bonding process where they were first bonded using a gold eutectic bond, then annealed at 1100 °C to allow gold diffusion into silicon and form what we call a gold diffusion eutectic bond. The gold diffusion eutectic-bonded micro-columns when examined using scanning electron microscopy (SEM), scanning acoustic microscopy (SAM) and blade insertion techniques showed bonding strength comparable to the previously reported anodic-bonded columns. Gas chromatography-based methane injections were also used as a novel way to investigate proper sealing between channels. A unique methane elution peak at various carrier gas inlet pressures demonstrated the suitability of gold diffusion eutectic-bonded channels as micro-GC columns. The application of gold diffusion eutectic-bonded all-silicon micro-columns to temperature-programmed separations (120 °C min⁻¹) was demonstrated with the near-baseline separation of n-C₆ to n-C₁₂ alkanes in 35 s.