Objectives: Chronic diseases require a multidisciplinary approach to provide optimal patient care in general practice. In Australian general practice, this usually involves referral to an allied health provider outside the practice. This study explored the patient and practice factors associated with referral of patients with diabetes, ischaemic heart disease (IHD) or hypertension to external allied health providers (AHPs). Methods: A multilevel analysis of data collected as part of a quasi-experimental study was conducted in 26 practices in Sydney. The frequency of patient-reported referral to AHPs 6-months post-intervention was measured against patient and practice characteristics assessed by patients and practice staff questionnaires. Findings: Seven per cent of the total variance in the referrals was due to differences between practices and 93% attributed to differences between patients. Previous referral, age over 45 years, multiple conditions, longer illness duration, poor mental and physical health were associated with the likelihood of referral to AHPs but not socio-economic status, patient self-assessment of care and the intervention. Those attending practices with over three GPs were more likely to be referred. Conclusions: Referral to multidisciplinary care for patients with long term conditions was appropriately linked to the complexity, duration and impact of these conditions. The lack of association between the intervention and the frequency of referral suggests that factors other than knowledge and communication such as the accessibility of the allied health services may have been more important in determining referral.