Previous reports suggest that activated clotting times do not correlate with heparin concentration during cardiopulmonary bypass. This study was designed to compare whole blood heparin concentration and activated clotting time measurements with laboratory-based plasma heparin concentration. Sixty-two patients having cardiac operations requiring cardiopulmonary bypass were enrolled in this study. The study was conducted in two phases. In phase I of this trial, blood specimens were obtained from 30 patients before heparin administration and after each of three heparin doses (20, 80, and 150 U/kg). In phase II, blood specimens were obtained from 32 patients before heparin administration and 10 minutes after each of the following: heparin administration (250 or 300 U/kg), initiation of cardiopulmonary bypass, achievement of hypothermia, initiation of rewarming, and immediately before discontinuation of bypass. Blood specimens were used to measure activated clotting time (kaolin and celite), whole blood heparin concentration, and anti-factor Xa plasma heparin concentration. In phase I, activated clotting time (celite: r = 0.91; kaolin: r = 0.93) and whole blood heparin concentration (r = 0.98) measurements correlated well with plasma heparin concentration. After initiation of cardiopulmonary bypass (phase II), weak correlations for activated clotting time measurements (celite: r = 0.34; kaolin: r = 0.59) and a strong correlation for whole blood heparin concentration (r = 0.95) were evident when compared with plasma heparin concentration. During bypass, activated clotting time measurements also inversely correlated with temperature (celite: r = -0.21; kaolin: r = -0.19) and hematocrit (celite: r = -0.26; kaolin: r = -0.21). A weak correlation between activated clotting time measurements and plasma heparin concentration is evident during the cardiopulmonary bypass period, probably because of the influence of both reduced hematocrit and temperature on the activated clotting time assay. In contrast, whole blood heparin measurements correlate well with plasma heparin concentration before and during bypass. Further studies are needed to determine whether maintaining heparin levels during cardiopulmonary bypass by monitoring heparin concentration is more effective in preventing consumptive activation of the hemostatic system, reducing bleeding, and minimizing the use of blood products after cardiopulmonary bypass when compared with a protocol based on activated clotting time.