Objectives: The aim of this study was to investigate the prevalence of metabolic syndrome, in children with type one diabetes mellitus (T1DM) for the first time in a population in the Middle East, and assess the influence of type of insulin therapy, daily dosage of insulin, family history of type 2 diabetes, gender and level of HbA1c on the prevalence of metabolic syndrome. Methods: This cross-sectional study was conducted on children with T1DM aged < 20 years, and duration of T1DM >2 years during years 2013 to 2014. Waist circumference, blood pressure, height and weight of children with diabetes, for calculation of body mass index (BMI), were measured by one physician. Fasting blood glucose and lipids were also measured. According to the age-modified standards of the ATPIII, metabolic syndrome was defined. All data were analyzed using the SPSS 18 software. Results: In this study, 87 children with diabetes (48 females and 39 males) aged 12.38 ± 4.2 were enrolled. Overall, 40.9% of our patients had hypertension, 55.2% had hypertriglyceridemia, 36.8% had low high-density lipoprotein (HDL) and 6.9% of patients had abdominal obesity. Furthermore, 29.9% of these children had metabolic syndrome, which did not have a significant association with the type of insulin regimen (P = 0.97), nor the daily dosage of insulin (P = 0.234), however the serum concentration of HbA1c had a significant correlation with metabolic syndrome (P = 0.027). Conclusions: This study provides evidence indicating high prevalence of metabolic syndrome in children with T1DM in southern Iran. Preventive programs aimed towards decreasing the risk factors of metabolic syndrome and interpretation of a healthier diet and physical activity for children with T1DM should be considered in our country.