BackgroundThe metabolic syndrome (MetS) and its components are well-established risk factors for cardiovascular diseases (CVD). It is inconclusive whether MetS and MetS score are associated with electrocardiographic markers of subclinical CVD, therefore we investigated this in a population without pre-existing CVD.MethodsWe performed a cross-sectional analysis in the Netherlands Epidemiology of Obesity study, a population-based cohort including 6671 participants aged 45–65. We excluded participants with pre-existing CVD (n = 499) or missing MetS components (n = 58). MetS was defined based on a modified definition of Adult Treatment Panel III. Subclinical CVD parameters were determined with 12-lead ECGs. MetS score was defined as number of abnormal MetS components and obesity as Body Mass Index (BMI) ≥30 kg/m2. We performed weighted adjusted linear regression analyses.ResultsOur study population (n = 6114) had a mean (SD) BMI of 26.3 (4.4) kg/m2 and MetS was present in 24% of participants. All ECG parameters differed between participants with and without MetS. Per additional MetS component, heart rate was 0.17 SD (95% CI 0.15, 0.19) higher, P wave duration, QRS complex duration and corrected QT interval were longer [0.07 SD (0.05, 0.10), 0.04 SD (0.01, 0.06) and 0.05 SD (0.02, 0.08) respectively], P wave axis, T wave axis and QRS axis were lower [−0.10 SD (−0.12, −0.07), −0.07 SD (−0.10, −0.05) and −0.19 SD (−0.22, −0.16)] and percentage small Q-waves also increased per additional MetS component. Associations were stronger in non-obese than obese participants. In joint modelling of all MetS components, increased waist circumference showed strongest associations with ECG parameters.ConclusionsMetabolic syndrome score and its individual components, in particular abdominal obesity, are associated with ECG markers of subclinical CVD, showing the importance of limiting the amount of MetS components in both obese and non-obese persons.Electronic supplementary materialThe online version of this article (doi:10.1186/s13098-017-0238-9) contains supplementary material, which is available to authorized users.