Processing of cassava roots by the Alur tribe in Uganda includes a stage of solid substrate fermentation in heaps. Changes in cyanogen levels during the process, microflora involved, and protein levels, amino acid patterns and mycotoxin contamination of the final products were studied. Processing was monitored at six rural households and repeated at laboratory site, comparing it to sun-drying. Flour samples from rural households were analysed for residual cyanogens, mutagenicity, cytotoxicity and aflatoxins. Mean (±SD) total cyanogen levels in flours collected at rural households were 20.3 (±16.8) mg CN equivalents kg−1dry weight in 1990 (n= 23) and 65.7 (±56.7) in 1992 (n= 21). Mean (±SD) levels of cyanohydrins plus HCN were 9.1 (±8.7) in the 1992 flours. Total cyanogen levels in the village monitored batches were reduced considerably by heap-fermentation from 436.3 (±140.7) to 20.4 (±14.0) mg CN equivalents kg−1dry weight cassava. Residual cyanogen levels were positively correlated with particle size of the resulting crumbs. Heap-fermentation was significantly more effective in reducing cyanogen levels than sun-drying alone, but did not always result in innocuous levels of cyanogens. Dominant mycelial growth was from the fungiNeurospora sitophila, Geotrichum candidum and Rhizopus oryzae. No mutagenicity, cytotoxicity nor aflatoxins could be detected in the flours. Protein quantity and quality were not significantly reduced. Cassava gel viscosity pattern was modified to the consumers' preference by this method. As the removal of cyanogens was more efficient and we found no new obvious health risk, heap-fermentation can be regarded as an improvement compared to sun-drying alone in areas where cassava varieties with higher cyanogen levels prevail, but we recommend optimisation of the process for ensuring still safer products.