Background Studies have shown that complications in type 1 diabetes mellitus (T1DM) in children are mainly due to oxidative stress (OS). Lipid peroxidation is the main marker of OS and iso-prostaglandin is a reliable biomarker of lipid peroxidation in type 2 diabetes mellitus (T2DM). However, there have been few studies on OS in T1DM children with hyperglycemia and glucose fluctuations. Methods We prospectively enrolled 23 newly diagnosed T1DM patients and 23 age and sex matched healthy controls in Beijing Children's Hospital from May 2010 to January 2011. They were treated with continuous subcutaneous insulin injection (CSII) and monitored by continuous glucose monitoring system (CGMS). Twenty-four-hour urine samples were collected to measure the concentration of 8-iso prostaglandin F2 alpha (8-isoPGF2 alpha). Samples taken from diabetic children were collected at days 8 to 10 after insulin treatment. Intraday glucose fluctuations were assessed by mean amplitude of glucose excursions (MAGE), largest amplitude of glycemic excursions (LAGE), standard deviation of blood glucose (SDBG) and number of glycemic excursions (NGE). The correlations between glucose parameters and the index of oxidative stress were analyzed. Results Urine 8-isoPGF2 alpha in the T1DM group was higher than that in the control group ((967.70 +/- 412.68) ng vs. (675.23 +/- 354.59) ng, P=0.019). There was a correlation between urine 8-isoPGF2 alpha level and MAGE (r=0.321, P=0.039), a significant correlation between low-density lipoprotein and urine 8-isoPGF2 alpha level (r=0.419, P=0.03). There was no significant correlation between urine 8-isoPGF2 alpha level and blood pressure, glycosylated hemoglobin (HbA1c), fasting C-peptide or other lipid indices. Conclusion A correlation between urine 8-isoPGF2 alpha levels and MAGE and low-density lipoprotein was found in children newly diagnosed with T1DM.