The isotope pairing technique (IPT) is a well-established N-15 method for estimation of denitrification. Presence of anammox, the anaerobic oxidation of NH4+ to N-2 with NO2- results in violation of central assumptions on which the IPT is built. It is shown that anammox activity causes overestimation of the N-2 production calculated by the IPT. However, experiments with different additions of (NO3-)-N-15 will reveal the problems posed by anammox. Two alternative calculation procedures are presented, which enable a more accurate quantification of anammox and denitrification activity in sediments where the processes coexist. One procedure is based on measurements of N-15-N-2 production in (NOx-)-N-15-amended intact sediment cores and data addressing the contribution of anammox to total N-2 production estimated from slurry incubations. The other procedure is based on measurements of N-15(2) production in at least two parallel series of sediment cores incubated with different (NOx-)-N-15 additions. The calculation procedure presented is used on field data from four studies where the IPT was used and the potential anammox rate measured. The IPT overestimated total N-14-N-2 production rates by 0%, 2.5%, 31%, and 82% relative to the revised estimates from the 4 different sites, where anammox accounted for 0%, 6%, 18%, and 69.8%, respectively, of N-2 production. The overestimation of true denitrification was, however, up to several hundred percent. Our analysis suggests however that the IPT does not seriously overestimate N-2 production in estuarine sediments because anammox accounts for <6% of N-2 production in such sediments, according to present knowledge.