Robust, high temperature micro-reactors for online conversion of organic compounds were microfabricated in high purity fused silica to enable stable isotopic compositional analysis of individual compounds in mixtures using advanced gas chromatography (GC) separation techniques, such as fast GC and comprehensive 2D GC, coupled to isotope ratio mass spectrometry (IRMS). These microreactors could also be manufactured at larger channel dimensions to enable robust operations for normal GCC-IRMS applications. Photolithography was used to define the reactor channel pattern on high purity fused silica, with a protective layer of amorphous silicon. A two-step isotropic wet etching process, using 49% HF, selectively created semi-circular cross-section micro-channels of arbitrary diameters (56-209 lm), with tapered sections leading to input/output ports ([400 lm) that accept fused silica capillary tubing used in GC and MS peripherals. Pairs of symmetric mirror image substrates were aligned and bonded to form enclosed circular channels. The resulting micro-reactors are more robust than the standard designs made of fragile-fused silica capillary or alumina tubes of relatively large bore, and are gas tight at temperatures up to 1,000°C. Fast GC plugs of CH 4 with and without the reactor revealed that peak shapes are minimally affected by the micro-reactor when carrier flow rate and channel diameter are optimized. Peak shapes with full widths at half maximum of 250 ms are shown for plugs of CH 4 through a fast-GC-combustion-IRMS system interfaced with a micro-reactor containing a CuO/NiO combustion source, enabling carbon isotope ratio measurements of CH 4 with a precision of SD(d 13 C) = ±0.28%. The devices enable arbitrarily narrow bores and long path channels that can be operated as open tubes or loaded with a reactant, in a small, robust package.