Complementary and alternative medicine are treatments administered alone or in combination with conventional medical treatments. Data on complementary and alternative medicine use in children with kidney and urinary tract diseases are limited. In this cross-sectional study, the frequency and preferred methods of complementary and alternative medicine use and factors associated with their use were evaluated in 201 patients (48% female; median age, 11 years; median disease duration, 5.1 years) with kidney and urinary tract diseases and 260 healthy (without chronic disease) controls. Data were collected through a questionnaire-based interview and patients' medical records. Herbal and dietary supplements, including fish oil, were the most commonly used complementary and alternative medicine agents in both groups. There was no difference in herbal and dietary supplement use between the groups when fish oil was excluded (29% vs. 28%;p = 0.88). Herbal and dietary supplements were mainly used to improve/mitigate renal disease (52%). Logistic regression analysis revealed that disease duration > 7 years (odds ratio (OR), 3.70; 95% confidence interval (CI), 1.48-9.20), current use of six or more drugs (OR, 5.6; 95% CI, 1.28-24.41), and recurrent urinary tract infection or nephrolithiasis (OR, 3.92; 95% CI, 1.02-15.09) were the independent risk factors for herbal and dietary supplement use, except fish oil. Middle socioeconomic status was associated with decreased herbal and dietary supplement use, except fish oil, compared with low socioeconomic status (OR, 0.30; 95% CI, 0.11-0.81). Herbal and dietary supplements were used by 78% patients, despite knowing that these products could have side effects; only 42% of the patients shared the information about herbal and dietary supplement use with their doctors.