In developing countries which are dependent on agriculture, value addition through local agro processing is always encouraged as a way to achieve economic growth and gaining of international competitiveness. A successful and sustainable growth and development of an agricultural nation such as Uganda would largely depend on value addition using good manufacturing practices and technologies that are efficient, effective, price sensitive and responsive to market needs in addition to product quality and safety requirements . To this end, the purpose of this study was to assess the extent and impact of standardization in the agro-processing Small and Medium Enterprises (SMEs) in Uganda with specific focus on indigenous maize processing mills and the quality of their flour output. This was done through assessing the level of standardisation based on a specified criterion guided by the US 28 EAS 39 standard guidelines on Code of practice for Hygiene in the Food and Drink Manufacturing Industry that was developed in form of a checklist, product testing and analysis based on Uganda product standards as well as open ended discussions with experts in the field of Quality. The data obtained by the checklist was analyzed using SPSS while the one from test results was interpreted using descriptive statistics to bring to order the research findings. The findings indicate minimal levels of input material, human element and methods, GMP, GHP, equipment/technological standardization among local maize processing SMEs and maize mill fabricators. The experimental results revealed that maize flour from locally fabricated maize mills did not pass the test for quality as it tested positive for extraneous matter (Iron filings) with an average net of 1.8 mg/kg of iron content. Key factors affecting standardizations among maize processing SMEs were found to include lack of control of source of raw materials, negative attitudes to standardization, low enforcement of standards, lack of awareness, costs and information gaps. The findings of the study suggest that there is need to modify the designs of locally fabricated mills to include provisions that eliminate the extraneous matter in the final processed maize flour to guarantee safety of the consumers. Also, it suggests that adoption of standardization practices such as certifications of inputs, equipment and processes would improve product safety and quality hence enhance competitiveness of these agro-processing SMEs on the local and international market.Makerere University