The study assessed the hazards and risks associated with micro, small and medium scale enterprises (MSMEs) in Nigeria. Checklists, interviews and risk assessment matrix were used to identify hazards, health implications and rating of associated risks. It was found out that the following hazards are prominent in Nigeria MSMEs; gaseous emission, fire, noise, vibration, radiation, heat, electrical connections, manual handling, loading, lifting, poor chemical handling, adulterated production formula, lack of training, poor ventilation, poor illumination, lack of safety signs, poor housekeeping, poor hygiene, weak construction, overloading, over stress, over pressure, ageing, bad process controls, systems, unguarded stationary and moving part, solid and liquid waste, wrong action, carelessness, under aged personnel, wrong instruction, over dosing, microbial growth, corrosion, hot liquid and solid, dust & particulates, bad stacking, sharp objects, leakage, confined space, explosion, reptiles, poisonous animals and wrong use of tools. It was recommended that, Management of MSMEs adopt and adapt the HSE-MS as a significant management tool, government, training institutions, researchers, NGOs and civil right organizations raise more awareness on the implementation of HSE-MS by MSMEs.