Unfractionated heparin (UFH) monitoring is subject to substantial inter-laboratory variation. We analysed results of annual coagulation surveys administered by the Quality Management Program – Laboratory Services (Toronto, ON, Canada) from 2003 to 2007 to evaluate variation in UFH monitoring across Ontario. Participating laboratories performed an activated partial thromboplastin time (APTT) utilising their local methodology on lyophilised human plasma spiked with UFH. In the 2006 and 2007 surveys, laboratories licensed to perform anti-Xa assays also reported anti-Xa activity results. The APTT differed significantly between heparin-sensitive and heparin-insensitive methods (p<0.0005). Within-method variation was observed and increased with increasing heparin concentration. Among laboratories performing an APTT and anti-Xa, the coefficient of variation was greater in the anti-Xa than in the APTT for both the 2006 (64.0% vs. 10.5%) and 2007 (15.0% vs. 11.6%) surveys. Substantial interlaboratory variation in UFH monitoring, both between and within APTT methods, was observed and was not reduced by use of an anti-Xa assay.