Background: As patients move across different clinical settings, medication changes are likely to occur. Aim: To identify patient-, medication- and environment-related factors associated with unintentional medication discrepancies in older patients, who were admitted to hospital via an emergency department and who had a subacute care admission at some point following hospital admission. Methods: A retrospective clinical audit was undertaken using a stratified random sampling approach over a 14-month period. Medical records of patients aged 65 years or over were collected from five hospitals. Findings: Data were collected from 426 older patients. Of these patients, 169 (39.7%) had at least one unexplained medication discrepancy. Patients without social supports had 2.956 greater odds of experiencing an unexplained medication discrepancy (95% CI 1.870-4.671), p<0.0001. As the number of prescribed medications increased upon admission to the emergency department, patients had 1.125 greater odds of experiencing an unexplained medication discrepancy (95% CI 1.035-1.223), p=0.006. Patients discharged to destinations other than their home had 2.714 increased odds (95% CI 1.317-5.594), p=0.007 while those experiencing more than four transition points of care had 2.476 increased odds (95% CI 1.208-5.074), p=0.013, of experiencing an unexplained medication discrepancy. A significant association existed between the prevalence of unexplained medication discrepancies and hospital readmission within six months, χ2 =36.496, df=1, p<0.001. Conclusion: Great care is needed in managing complex medication regimens of older people with multiple chronic conditions, especially those who move across several transition points of care.