To determine the relationship between the activated partial thromboplastin time (aPTT) measured with a standard laboratory assay and the aPTT measured with a bedside device in infants on heparin therapy after cardiothoracic surgery. Twenty infants aged below 1 year who were on heparin therapy were included. Exclusion criteria were prematurity, dysmaturity and the use of anticoagulants other than heparin. Nineteen samples were obtained from four adults in intensive care who were on heparin. The aPTT values were analyzed with the Coaguchek Pro/DM bedside device (aPTTbed) and compared with the aPTT values obtained from the laboratory Electra 1800C coagulation analyzer (aPTTlab). Correlation analysis was performed by linear regression. The agreement was calculated using Bland–Altman analysis. The correlation coefficient of samples obtained from infants was lower (r = 0.48) compared with samples from adults (r = 0.85). A substantial positive bias (27 s) and scatter [95% confidence interval (CI) −11; +65 s) was found. The bias showed a genuine trend to increase at higher aPTT values (r = 0.90; P < 0.001). The bedside device overestimates the aPTT in infants treated with heparin. The disagreement between the bedside device and laboratory increases at higher aPTTs. Bedside devices should not be used to monitor heparin therapy in infants in intensive care.