Background: Unfractionated heparin is a high-risk medication, as serious adverse events may result from errors of use. Different practices and protocols for unfractionated heparin are used at the three district health boards in Auckland. Concern about the inadequacies of heparin use prompted a collaborative evaluation of adherence to unfractionated heparin protocols and to aid the formulation of solutions for process improvement. Aim: To evaluate the three district health boards' compliance with unfractionated heparin protocols, and to identify issues with prescribing and administration and the occurrence of adverse events. Method: A retrospective audit of all patients started on unfractionated heparin at the three district health boards was undertaken from March to June 2005. An audit tool was developed to evaluate compliance with 6 criteria of prescribing and administration common to each hospital protocol and data were collected on indication and occurrence of adverse events. Results: 61 patients were audited. 51% had a baseline activated partial thromboplastin time (aPTT) measured, 39% had an aPTT measured at 6 hours, 80% received a heparin loading dose (90% as per protocol), 85% received maintenance infusion dose and rate as per protocol and 35% had failed to reach target aPTT at 72 hours. None of the 6 criteria achieved 100% compliance. Conclusion: Compliance with the specified protocols was low. Systems changes have been identified that can improve the safety and effectiveness of unfractionated heparin use.