Abstract Isotope fractionation resulting from gas diffusion along a thermal gradient has always been considered entirely mass‐dependent. A previous report, however, showed that non‐mass‐dependent 17 O anomalies can be generated simply by subjecting O 2 gas in an enclosure to a thermal gradient. To explore the underlying mechanism for the anomalies, we tested the effect of gas pressure, duration of experiment, and geometry of the apparatus on the 17 O anomalies for O 2 as well as on the 33 S or 36 S anomalies for SF 6 gas. The results are consistent with our proposal that a previously ignored nuclear spin effect on gas diffusion coefficient may be largely responsible for generating the observed anomalies. This discovery provides clues to some of the puzzling non‐mass‐dependent isotope signatures encountered in experiments and in nature, including the triple oxygen or quadruple sulfur isotope heterogeneity in the solar system. Copyright © 2011 John Wiley & Sons, Ltd.