This was a screening study that aimed to determine the presence of nephrotoxic mycotoxins in urine samples from patients with chronic kidney disease of uncertain etiology in the North Central Province of Sri Lanka. The percentage detection of aflatoxins, ochratoxins and fumonisins in 31 patients were 61.29%, 93.5% and 19.4%, respectively. Geometric means of urinary aflatoxins and ochratoxins were 30.93 creatinine and 34.62 ng/g creatinine in chronic kidney disease of uncertain etiology stage 1-2 patients and 84.12 ng/g creatinine and 63.52 ng/g creatinine in unaffected relatives of patients. In chronic kidney disease of uncertain etiology stage 3-5 patients, geometric means of urinary aflatoxins and ochratoxins were 10.40 and 17.08 ng/g creatinine, respectively. Non-affected relatives of patients (n = 6) had comparable levels of these mycotoxins, but healthy Japanese individuals (n = 4) had lower levels than in Sri Lanka. The higher detection rate of urinary ochratoxins in Sri Lankans indicates that exposure is common in the region.