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Mannihot esculenta Crantz (Cassava) is the second highest producer of carbohydrates after sugarcane. However, some varieties have high levels of cyanogenic glycosides and therefore are potentially toxic for human consumption. Nyakatanegi is one of the local varieties cultivated in Bar-agulu village in Siaya County (Kenya) and has been severally in the recent past reported to cause fatal cyanide toxicity. The other variety which is rarely associated with cassava poisoning is Mariwa. The objective of the current study was to determine cyanide levels in the two cassava varieties (Mariwa and Nyakatanegi) which are locally cultivated in Siaya County. The study was based on three laboratory assays: the picrate paper, picrate in solution and titration. Whole root cassava tubers were collected from a farmer in Bar-agulu village, Siaya County, packaged separately and transported to Mount Kenya University Pharmaceutical Chemistry Laboratory for analysis. Voucher specimens were authenticated in the cassava laboratories at Jomo Kenyatta University of Agriculture and Technology. It was observed that all the cortex samples of Nyakatanegi variety had the highest concentrations of cyanide giving 400 ppm for the picrate paper assay, 14.10 mg/Kg for the picrate in solution and 63 mg/Kg for the titration assays. On the other hand, the cortex samples of Mariwa reported cyanide concentrations of 30 ppm, 11.20 mg/Kg and 27.20 mg/Kg for the picrate paper, picrate in solution and titration assays respectively. The results showed higher amounts of cyanide in the tested cassava varieties than the WHO recommended levels (10 mg/Kg) especially the Nyakatanegi variety. Based on these results, sensitization campaigns are necessary to minimize cases of cyanide poisoning following cassava consumption.