There is controversy about the effect of certain drugs on cystatin C (CysC) concentrations, which would limit the usability of CysC for estimation of glomerular filtration rate (GFR) in patients with renal disease. Seventy-one children (ages 2.6 months to 18 years) with renal disease and on at least one study medication (tacrolimus, cyclosporine, mycophenolate mofetil, corticosteroids, fosinopril, ramipril and enalapril, losartan, cotrimoxazole) were tested in 85 nuclear medicine GFR clearance studies with simultaneous CysC determinations. We analyzed the relationship between the dose per kilogram and the ratio of the measured GFR to the CysC-derived GFR, with a ratio of 1 resembling agreement. A non-zero slope in linear regression analysis was considered significant for a drug effect on CysC. No significant relationship was found between the doses of the medication and the cystatin C GFR for any of the medications. Only cotrimoxazole showed a GFR ratio that was significantly lower than 1, which may be related to small numbers; otherwise the value was always 1. CysC provides accurate data for calculating GFR independent of the drug doses studied and avoids the use of methods of direct GFR measurement.