BackgroundMetabolic syndrome (MetS) is one of the main reasons for elevated cardiovascular morbidity and mortality worldwide. Obese and overweight individuals are at high risk of developing these chronic diseases. The aim of this study was to characterize and establish sex-adjusted prevalence of metabolic syndrome and its components.MethodsA cross-sectional study was conducted in 2015, 689 (329 men and 360 women) aged 18–65 years from three refugee camps in the West Bank. International Diabetes Federation and modified National Cholesterol Education Program-Third Adult Treatment Panel definitions were used to identify MetS.ResultsThe overall prevalence of obesity and overweight was high, 63.1%; Obesity (42 and 29.2% in women men; respectively and overweight 25.8 and 28.9% in women and men; respectively. The prevalence of MetS among obese and overweight was significantly higher (69.4%) according to IDF than NCEP definition (52%) (p < 0.002) with no significant differences between men and women using both definitions; (IDF; 71.8% men vs. 67.6% women, and (NCEP/ATP III; 51.9% men vs. 52.2% women). The prevalence of MetS increased significantly with increasing obesity and age when NCEP criterion is applied but not IDF. The prevalence of individual MetS components was: high waist circumference 81.3% according to IDF and 56.5% according to NCEP, elevated FBS 65.3% according to IDF and 56% according to NCEP, elevated blood pressure 48%, decreased HDL 65.8%, and elevated triglycerides 31.7%. Based on gender differences, waist circumferences were significantly higher in women according to both criteria and only elevated FBS was higher in women according to IDF criteria. Physical activity was inversely associated with MetS prevalence according to NCEP but not IDF. No significant associations were found with gender, smoking, TV watching, and family history of hypertension or diabetes mellitus.ConclusionIn this study, irrespective of the definition used, metabolic syndrome is highly prevalent in obese and overweight Palestinian adults with no gender-based differences. The contribution of the metabolic components to the metabolic syndrome is different in men and women. With the increase of age and obesity, the clustering of metabolic syndrome components increased remarkably. More attention through health care providers should, therefore, be given to the adult population at risk to reduce adulthood obesity and subsequent cardiovascular diseases.Electronic supplementary materialThe online version of this article (10.1186/s13098-018-0337-2) contains supplementary material, which is available to authorized users.