Metabolic syndrome is an important cause of cardiovascular disease. Mortality from cardiovascular disease is 12.82 deaths/100 000 population in Zahedan, south-east Islamic Republic of Iran. This study aimed to determine the incidence of metabolic syndrome and its predicting factors in Zahedan city. All participants without metabolic syndrome in a 2009 study in Zahedan, available in 2017, were included in this study. Metabolic syndrome was diagnosed based on the criteria of several organizations. Anthropometric indices and blood pressure were measured and blood tests were done. Age-standardized incidence of metabolic syndrome was calculated and its predictors were evaluated in a logistic regression analysis. Mean age (standard deviation) of the participants was 45.46 (12.63) years in 2017. The incidence of metabolic syndrome varied from 17.21% to 27.18% depending on the criteria used and it was higher in women. High age-standardized incidence was associated with large waist circumference (55.81%) and high blood pressure (25.32%). The highest adjusted odds ratios (OR) for metabolic syndrome were for high triglycerides (OR = 23.75; 95% confidence interval (CI): 9.92-56.84%), large waist circumference (OR = 22.42; 95% CI: 9.03-55.70%), high blood pressure (OR = 16.91; 95% CI: 8.54-33.50%) and high fasting blood sugar (OR = 13.22; 95% CI: 6.74-25.94%). Waterpipe smoking, sex, low-density lipoprotein and wrist circumference were also associated with metabolic syndrome. The incidence of metabolic syndrome has increased in Zahedan. Effective, interventions, including to promote healthy diet, physical activity and avoidance of waterpipe smoking, are needed to control this condition.