Abstract Secondary ion mass spectrometric (SIMS) measurements of sulfur isotope ratios obtained during sputtering with a Cs + beam and detection of negative secondary ions show a strong dependence of isotope fractionation on secondary ion energy for ions with ∼2–10 eV excess kinetic energy (∼9‰/eV), and a weak dependence for ions with ∼10–∼350 eV (0.05‰/eV). Variable collection of the low‐energy ions could thus result in variable measured sulfur isotope ratios. Being aware of this behavior should allow the analyst to avoid such a problem. The fractionation of the isotopes does not appear to follow theoretical or measured behavior for positive ions, and suggests that, at least for sulfur, the process of negative secondary ion emission is incompletely understood and may require different theoretical models. Copyright © 2002 John Wiley & Sons, Ltd.