Dairy value chains link the actors and the activities involved in delivering milk and milk products from production to the final consumer. In every activity, the product increases in value from production, transportation, processing, packaging and storage. The study was designed to evaluate some hygienic practices along the value chain and develop the quality control system (CCPs) in the smallholder supply chain in Nakuru and Nyandarua County, Kenya. To assess the level using critical control points of compliance to hygienic code of practice, the questionnaires were developed and pre-tested before being administered to the selected individuals in the study. Descriptive statistics was used to depict the implementation of the code of hygienic practices in milk handling by the farmers, transporters, collection and bulking enterprises (CBEs) and the processor. Among the various aspects investigated at farm level in this study was, hand washing before milking, use of reusable udder cloth while milking, use of plastic containers in milk delivery, time taken to deliver milk, cleaning of the cow shed and awareness of the antibiotic resides in milk and its effect. The results indicated poor conformance to the hygienic code of practice along the dairy value chain in the smallholder supply system. The various factors that could contribute to raw milk quality deterioration were identified as, the critical control points (CCPs) using the hazard analysis critical control points (HACCP) principles. Seven factors were identified at five critical points along the milk collection chains. The critical control points identified includes milking at the farm level, bulking milk in a fifty liters can at collection points, transportation, at the CBE platform and the cooling tank. The quality of raw cow's milk produced and marketed from the study areas was low.