Chronic Kidney Disease of unknown etiology (CKDu) has escalated into an epidemic in North Central Province (NCP) and adjacent farming areas in the dry zone of Sri Lanka. Studies have shown that this special type of CKD is a toxic nephropathy and arsenic may play a causative role along with a number of other heavy metals. We investigated the hypothesis that chemical fertilizers and pesticide could be a source of arsenic. 226 samples of Fertilizers and 273 samples of pesticides were collected and analyzed using atomic absorption spectrometry and inductively coupled plasma mass spectrometry for arsenic and other heavy metals in two university laboratories. Almost all the agrochemicals available to the farmers in the study area are contaminated with arsenic. The highest amount was in triple super phosphate (TSP) with a mean value of 31 mg/kg. Also TSP is a rich source of other nephrotoxic metals including Cr, Co, Ni, Pb and V. Annually more than 0.1 million tons of TSP is imported to Sri Lanka containing approximately 2100 kg of arsenic. The next highest concentration was seen in the rock phosphate obtained from an open pit mine in NCP (8.56 mg/kg). Organic fertilizer contained very low amounts of arsenic. Arsenic contamination in pesticides varied from 0.18 mg/kg to 2.53 mg/kg although arsenic containing pesticides are banned in Sri Lanka. Glyphosate the most widely used pesticide in Sri Lanka contains average of 1.9 mg/kg arsenic. Findings suggest that agrochemicals especially phosphate fertilizers are a major source of inorganic arsenic in CKDu endemic areas. Organic fertilizer available in Sri Lanka is comparatively very low in arsenic and hence the farmers in CKDu endemic areas in Sri Lanka should be encouraged to minimize the use of imported chemical fertilizer and use organic fertilizers instead.