BackgroundThe civil war in Syria including the deliberate targeting of healthcare services resulted in a complex humanitarian emergency, seriously affecting children's health. The objectives of this study are to document diagnoses and disease categories in Northern Syrian children after four years of conflict, and to document infectious diseases and injuries in this vulnerable population.MethodsIn a prospective cross-sectional observational sample study conducted in May 2015, healthcare workers registered demographics, comorbidities, and diagnoses (categorised according to the International Classification of Diseases version 10) in children visited at home and in internally displaced persons camps in four Syrian governorates.ResultsOf 1080 filled-out records, 1002 were included. Children originated from Aleppo (41%), Idleb (36%), Hamah (15%) and Lattakia (8%). Median age was 6 years (0–15; IQR 3–11), 61% were boys, 40% were younger than 5 years old. Children suffered from respiratory (29%), neurological (19%), digestive (17%), eye (5%) and skin (5%) diseases. Clinical malnutrition was seen in 4%, accidental injury in 3%, intentional injury in 1%, and mental disorders in 2%. Overall, 64% had features of infectious diseases (OR 0.635; CI 0.605–0.665). Most common comorbidities were chronic respiratory diseases (14, malnutrition (5%), acute flaccid paralysis (5%), and epilepsy (4%). Logistic regression analysis indicated that the risk for children to have communicable diseases was higher in Aleppo than in Idleb (OR 1.7; CI 1.2–2.3), Hamah (OR 4.9; CI 3.3–7.5), or Lattakia (OR 5.5; CI 3.3–9.3). Children in Aleppo and Lattakia were more at risk to be injured than in Idleb (OR 5.6; CI 2.1–14.3), or in Hamah (OR 5.9; CI 1.4–25.6), but more often from intentional violence in Lattakia. Mental problems were more prominent in Hamah.ConclusionsFour years far in the conflict, 64% of the studied children in four Northern Syrian governorates suffer from infections, mostly from respiratory, neurological and digestive origin, while 4% was injured or victim of intentional aggression. Substandard living conditions and the lack of paediatric healthcare put Syrian children at risk for serious infections, epidemics and morbidity, and ask for urgent international humanitarian relief efforts.