An experimental study was conducted to assess the pathogen removal efficiency of primary treatment of ecological sanitation (eco-san) system. Ash, lime and soil were used as covering and treatment materials of faeces in the system. A significant rise in pH was observed when the faeces were treated with lime and ash, with a pH value of 11.3 and 9, respectively. Lime treatment was effective in complete destruction of faecal coliforms within 24 h while ash treatment took 30 days of storage to give the same result. On the other hand, no immediate destruction of Ascaris ova was observed during primary treatment of eco-san faeces. Dehydration and storage were other parameters which were considered in the experiment. Faecal coliforms tolerated a moisture content of 3% in untreated faeces while a large number of Ascaris lumbricoides eggs were inactivated by the same level of desiccation, even in the absence of alkaline treatment. The study showed a strong direct relationship between moisture content and viability of Ascaris egg (r = 0.806, p = 0.01) and a negative correlation between viability of eggs and storage time (r = -0.895, p = 0.01). Generally, the treatment methods used in this experiment showed a substantial potential of faeces sanitization, with removals ranging from 54 to 100% after a minimum of 40 days storage.