BackgroundThe Syrian armed conflict is the worst humanitarian tragedy this century. With approximately 470,000 deaths and more than 13 million people displaced, the conflict continues to have a devastating impact on the health system and health outcomes within the country. Hundreds of international and national non-governmental organisations, as well as United Nations agencies have responded to the humanitarian crisis in Syria. While there has been significant attention on the challenges of meeting health needs of Syrian refugees in neighbouring countries such as Jordan, Lebanon and Turkey, very little has been documented about the humanitarian challenges within Syria, between 2013 and 2014 when non-governmental organisations operated in Syria with very little United Nations support or leadership, particularly around obtaining information to guide health responses in Syria.MethodsIn this study, we draw on our operational experience in Syria and analyse data collected for the humanitarian health response in contested and opposition-held areas of Syria in 2013–4 from Turkey, where the largest humanitarian operation for Syria was based. This is combined with academic literature and material from open-access reports.ResultsHumanitarian needs have consistently been most acute in contested and opposition-held areas of Syria due to break-down of Government of Syria services and intense warfare. Humanitarian organisations had to establish de novo data collection systems independent of the Government of Syria to provide essential services in opposition-held and contested areas of Syria. The use of technology such as social media was vital to facilitating remote data collection in Syria as many humanitarian agencies operated with a limited operational visibility given chronic levels of insecurity. Mortality data have been highly politicized and extremely difficult to verify, particularly in areas highly affected by the conflict, with shifting frontlines, populations, and allegiances.ConclusionsMore investment in data collection and use, technological investment in the use of M- and E-health, capacity building and strong technical and independent leadership should be a key priority for the humanitarian health response in Syria and other emergencies. Much more attention should be also given for the treatment gap for non-communicable diseases including mental disorders.