This paper presents evidence from research into health system challenges of cardiovascular disease (CVD) and diabetes in four Eastern Mediterranean countries: the occupied Palestinian territory, Syria, Tunisia and Turkey. We address two questions. How has the health system in each country been conceptualised and organised to manage the provision of care for those with CVD or diabetes? And what were key concerns about the institutional ability to address this challenge? Research took place from 2009 to 2010, shortly before the political upheavals in the region, and notably in Syria and Tunisia. Data collection involved a review of key documents, interviews with key informants and brief data collection in clinics. In analysing the data, we adopted the analytical schema proposed by Walt and Gilson, distinguishing content, actors, context and process. Key findings from each country highlighted concerns about fragmented provision and a lack of coordination. Specific concerns included: the lack of patient referral pathways, functioning health information systems and investment in staff. Regarding issues underlying these 'visible' problems in managing these diseases, we highlight implications of the wider systemic pressure for reform of health-sector finance in each country, based on neoliberal models.