The aim of this study was to measure the effects of heparin therapy in patients undergoing vascular surgery, and to monitor the effectiveness of continuous intravenous heparin therapy in ward-based patients. In addition, we compared results from a new portable device with those from the standard laboratory assay. A prospective comparison of the two methods in patients undergoing peripheral vascular surgery, and in ward-based patients who were receiving intravenous heparin infusions was undertaken. Fifty patients who were undergoing vascular surgery and receiving a bolus dose of intravenous heparin, and 22 patients receiving a continuous heparin infusion, were recruited. Blood samples were taken 10 and 40 min following bolus heparin administration or after > 12 h of a continuous heparin infusion. Plasma activated partial thromboplastin times (APTTp) measured by the haematology laboratory were compared with whole blood (APTT(B)) ascertained with the CoaguChek Plus Device (Boehringer Mannheim UK Diagnostics and Biochemicals Limited) at each time point. The results from the two methods were compared using the method of Bland and Altman (Lancet, 1986, 307-310). We found a good level of agreement between the two methods (at induction, mean bias was -0.050, limits of agreement -0.46 - 0.36; heparin infusions, mean bias was -0.283, limits of agreement -1.64 - 1.07). In addition we discovered that many of our patients appeared to be excessively anticoagulated during surgery (10 min following heparin bolus 47/50 patients had an APTT(B) > 150 s, 45/50 had an APTTp > 250 s; at 40 min 45/50 had an APTT(B) > 150 s, 39/50 had an APTTp > 250 s). In conclusion, whole blood APTT measurement allows rapid and accurate assessment of the effects of heparin therapy when compared with laboratory APTT measurement and may prevent both excessive and suboptimal anticoagulation.