The sanitary quality of raw milk is an important issue in Uganda for social, economical and healthy reasons. A survey on milk quality was carried out in Mbarara major milk producing region in Uganda, between June and August 2004. The milk production system described in this paper has largely remained unchanged up to now. Milk quality was analysed at six stages of the commodity chain: farm, bicycle collector at the farm level, pick-up collecting centre, milk collecting centre, urban cooler, and vendor in Kampala city at the urban cooler level. Milk quality was evaluated using platform tests (Clot on boiling (COB), Alcohol test, milk temperature and density) and microbiological tests (total plate count, total and faecal coliforms, Escherichia coli count). Approximately half of the total coliform count was attributed to fecal coliforms including E. coli. This indicates great possibility of the occurrence of enteric pathogens in milk. This is partly confirmed by the large count of E. coli. The bacteria load reached very high levels close to 2 x 106 colony forming units per millilitre (cfu/mL) at the farm level, and these levels increased 150-fold during transportation to Kampala. An analysis of the raw milk marketed through the informal sub sector in Uganda, revealed two main issues: (i) poor hygiene conditions from the production location all the way to the consumer; (ii) lack of an efficient preservation system to limit bacteria proliferation during transportation to Kampala. Milk was overheated at the urban informal milk heat processing units but rendered free from bacteria. However, storage of such treated milk over several days makes this process potentially more dangerous than beneficial since post processing contamination of a sterile substratum could lead to rapid proliferation of microorganisms. Milk quality across the value chain could be improved through: (i) changing milking practices to ensure better hygienic conditions; (ii) improvement of milk handling an