Isotopic measurements at the micron scale using secondary ion mass spectrometry (SIMS) require an accurate control on the instrumental mass fractionation (IMF). The IMF correction is challenging since substantial mass fractionation can occur during both emission and detection processes. In this work, we report hydrogen isotopic measurements on a series of organic standards using polyatomic ions (CH-, CD-, C2H-, C2D-) with the NanoSIMS-50 instrument. We show that the D/H ratios resulting from the measurement of CD-/CH- and C2D-/C2H- ratios are close to the true D/H ratios of the samples over more than 3 decades and allow accurate hydrogen isotopic measurements to be performed in solid samples. Large secondary emission yields are usually associated with high electron affinities and correlate presently with low IMF effects. Moreover, we show that even when large variations in secondary ionic current are observed, an accurate isotopic ratio can still be inferred. (C) 2015 Elsevier B.V. All rights reserved.