It has been suggested that urinary glycosaminoglycans (GAGs) form a natural defense mechanism against urinary tract infections (UTIs). This study investigated whether urinary GAGs play a role in pediatric UTIs, and whether urinary GAG level can be used to differentiate upper UTI from lower UTI. Forty-one children with UTIs ( 33 girls and eight boys; mean age 5.4+/-3.7 years) and 46 age- and sex-matched healthy children ( 35 girls and 11 boys; mean age 6.6+/-3.9 years) were included in the study. Urinary GAG levels were measured at the onset of acute infection and after a 10-day course of antibiotic treatment. Group GAG findings were compared, and comparisons were also made with the patients divided according to sex and according to UTI type ( upper versus lower). The mean urinary GAG level in the patient group at the onset of acute infection ( pretreatment) was significantly higher than the mean level in the control group ( 132.2+/-104.8 mg/g vs 42.2+/-27.1 mg/g creatinine, respectively; P < 0.01). In the patient group, the mean urinary GAG level after antimicrobial therapy was significantly lower than the pretreatment level ( 75.9+/-52.1 mg/g vs 132.2+/-104.8 mg/g creatinine, respectively; P < 0.01). However, the mean post-treatment level was still higher than the mean level in the controls ( P < 0.05). There was no significant difference in urinary GAG levels when patients were categorized as upper versus lower UTI ( P > 0.05). The study results suggest that GAGs play an important role in the pathogenesis of UTIs in children, and that measurement of urinary GAGs may be a valuable noninvasive method for evaluating UTIs in this patient group. However, this assay cannot be used to differentiate upper UTI from lower UTI in children.