(18)O labeling is a well-known method for the stable isotope labeling of proteins and peptides. This study describes a modified procedure for using (18)O labeling on small molecules. Fumonisin B1, a worldwide occurring mycotoxin, which is routinely analyzed by HPLC-MS/MS, was chosen as model compound. (18)O labeling was achieved by acid-catalyzed oxygen exchange from H2(18)O. A mixture of different isotopologues was obtained from the exchange, which, however, could be used as an internal standard for HPLC-MS/MS analysis. The identity of the (18)O-labeled fumonisin B1 was confirmed by NMR and HRMS measurements. The applicability as internal standard has been verified by comparison of results obtained from the method described in this paper to results obtained by reference methods. The presented method is of special interest as the (18)O labeling can be generally applied to a large group of small molecules containing carboxylic groups.