Abstract Background Data on the prevalence of overweight and obesity in Eastern Mediterranean countries remain scarce, particularly for children and adolescents. The objective of this study is to estimate the prevalence of obesity and examine associated factors and covariates amongst school adolescents in Syria. Methods A cross-sectional survey of a representative sample of 776 adolescents (386 males and 390 females), aged 15-18 years, was conducted in six randomly chosen secondary schools in Damascus, the capital city of Syria. Anthropometric measurements and dietary assessment data were collected using standard methods and techniques. Overweight and obesity were defined according to World Health Organization 2007 child growth standards. Results The prevalence rates of overweight and obesity were estimated at 18.9 and 8.6%, respectively. Carbohydrate and saturated fatty acid intakes were significantly higher amongst overweight and obese (250.66 and 32.82 g/day, respectively) as compared with normal weight adolescents (218.12 and 26.10 g/day, respectively). Regression analysis showed that the likelihood of obesity was significantly greater amongst adolescent boys than girls (OR = 2.30, P < 0.05) and amongst subjects reporting family history of obesity (OR = 2.98, P < 0.05). The odds of obesity increased consistently with increasing educational attainment of both parents and was higher (OR = 1.63) amongst adolescents reporting lower crowding index than their counterparts. Conclusion Our findings of a positive association between obesity and socio-economic status measured by parental education and crowding index call for intervention strategies for the promotion of healthy dietary practices not only amongst school adolescents but also parents, targeting families as the unit of intervention. Further studies are needed to examine nutritional habits and food choices amongst families of different socio-economic strata.