Aims The purpose of this study was to characterize the relationship between the degree of anticoagulation, assessed by APTT, and the plasma concentration of inogatran in healthy subjects and in patients with coronary artery disease. Methods Data from ®ve phase I studies in 78 healthy males and two phase II multicentre studies in 948 patients of both sexes with unstable angina pectoris or non-Q-wave myocardial infarction were evaluated. A total of 3296 pairs of concentration-APTT samples were obtained before, during, and after intravenous infusions of inogatran. Mixed effects modelling was used for population pharmacodynamic analysis of the drug effect and for describing the variability in baseline APTT. Results The population mean baseline APTT was 29 s, but large variations between individuals (s.d. 3.6 s) were observed. The variability between studies (1.3 s) and centres (1.8 s) were of less importance, though statistically signi®cant. APTT increased in a nonlinear manner with increasing inogatran concentration and the relationship was well described by a combined linear and E max model. A signi®cant part of the overall variability could be ascribed to the APTT reagent and equipment used at the different study centres. These method-dependent differences were compensated for by including the lower limit of the normal reference range as a covariate, affecting both baseline and E max , in the model. For the typical healthy subject and patient, the method-corrected population mean parameters were: APTT baseline 35 and 31 s, slope 8.0 and 5.8 s l mmol x1 , E max 36 and 34 s, and EC 50 0.54 and 0.72 mmol l x1 , respectively. The model predicted plasma concentration needed to double the APTT from the baseline value was 1.25 and 1.45 mmol l x1 in the healthy volunteer and patient, respectively. Conclusions The nonlinear relationship between APTT and inogatran concentration in plasma was well described by a combined linear and E max model. Pooling of data was made possible by incorporating a centre-speci®c characteristic of the assay method in the model. Patients had lower baseline APTT and appeared to have less pronounced effect of inogatran than young healthy subjects.