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The aims of this paper are to present the findings of a process evaluation exploring the experiences and opinions of clinicians who have been involved in the HealthPathways Barwon clinical workgroups and discuss implications for further development of the program, as well as regional health service initiatives more broadly. HealthPathways Barwon is a web-based program comprising locally agreed-upon evidence-based clinical pathways that assist with assessment, management and region-specific referral for various clinical conditions. Clinical workgroup members participated in focus groups. Coding and thematic analysis were performed and findings were compared with similar evaluations of HealthPathways in other jurisdictions. Five broad themes emerged from the focus group, each with several subthemes: (1) purpose of HealthPathways; (2) workgroup process; (3) barriers and facilitators to HealthPathways use; (4) impact of HealthPathways on clinical practice; and (5) measuring performance. Findings of particular interest were that the perceived drivers for implementation of HealthPathways Barwon are broad, HealthPathways Barwon is viewed positively by clinicians, the workgroup process itself has a positive impact on relationships between primary and secondary care clinicians, existing habits of clinicians are a major barrier to adoption of HealthPathways Barwon, the sustainability of HealthPathways Barwon is a concern and it is difficult to measure the outcomes of HealthPathways. Although HealthPathways Barwon is viewed positively by clinicians and is seen to have the potential to address many issues at the primary-secondary care interface, successful implementation and uptake will depend on buy-in from clinicians, as well as continuous evaluation to inform improved development and implementation. More broadly, health service initiatives like HealthPathways Barwon require longer-term certainty of funding and administration to become established and produce meaningful outcomes.