AIM: The aim of this study was to determine the proportion of children less than 12 months of age presenting to Hunter New England (HNE) emergency departments (EDs) during 2009 who were overdue for immunisations and identify factors associated with overdue status. METHODS: The immunisation status of all children aged between 3 months and 1 year (120-365 days) who presented at an HNE ED between 1 January and 31 December 2009 was determined using Australian Childhood Immunisation Register (ACIR) 30-day overdue reports. The ED dataset and ACIR reports were linked using a deterministic method. RESULTS: Six per cent (253/4218) of children who attended an HNE ED in 2009 were overdue for immunisation and 28.1% (71/253) presented multiple times while overdue. There was a median delay of 77 days from their first presentation while overdue until they no longer appeared on the ACIR 30-day overdue report. Children who presented while overdue were more likely to present multiple times to EDs (RR = 1.45; P = 0.0025), be in a life-threatening triage category (P = 0.012) and present at tertiary referral hospitals (P < 0.001). CONCLUSIONS: Important missed immunisation opportunities occurred in HNE EDs and may occur in other EDs in Australia. Half of the children who presented to Hunter New England emergency departments while overdue for immunisation remained overdue for greater than 77 days following their presentation. Opportunities exist in EDs and paediatric inpatient wards for ensuring that all children are protected against vaccine-preventable diseases.