Radioactive decay during measurement can be accounted for by either a decay correction of the measured data before modeling (DbM) or by direct implementation of decay into the pharmacokinetic model (DiM). The purpose of this study was to quantify the influence of the type of decay correction on the calculated parameters for the example of a three-compartment model used for the calculation of myocardial perfusion with 13N ammonia and positron emission tomography (PET). For a given input function [Ca(t)infinity t exp(-kt), k= 1.72/min] the tissue uptake for two parameter sets of K1, k2, k3, TBV were calculated for 20 frames (12 x 10 s, 4 x 30 s, 3 x 120 s, 1 x 300 s). These values were mathematically deteriorated by various noise levels according to Poisson statistics and fitted by a Levenberg-Marquardt algorithm. Estimated parameter means and coefficients of variation of the fitted parameters were calculated for the DbM and DiM case. The estimated parameter means for both decay correction methods were of comparable quality. The important measure for a single fit is the relative variability of the fitted parameters. This value is up to a factor 1.15 smaller for K1 obtained with DiM and a reasonable noise level of 10%. Therefore, decay correction should be taken into account during modeling to reduce the variability in the fitted parameters.