Milk has tremendous nutritional value for both people and animals, but because it also contains water, many different kinds of microbes can develop in it. Dairy products are still sold in both regular and unofficial marketplaces in Rwanda. Significant dangers to human health are associated with milk sold in unregulated markets. The aim of the present study was to assess the bacteriological quality and associated risk factors of raw milk marketed in Nyagatare district, Rwanda. 126 samples were collected among milk transporters from 14 sectors of Nyagatare district, Rwanda, where 9 samples were taken from each sector and analyzed in veterinary microbiology lab of University of Rwanda, Nyagatare campus. The bacterial analysis was based on carrying out total bacterial count, Coliform count, enumeration of Staphylococcus species and enumeration of Salmonella species. Milk transportes were also asked about risk factors associated with bacterial contamination of raw milk. The total bacterial count, Coliform count and enumerated Staphylococcus species had range from 7.8 × 104- 80 × 104cfu/mL, 24 × 101and 80 × 101cfu/mL and 20.8 × 101and 211 × 101cfu/mL respectively and highest prevalence of Salmonella to be 1.58%. The level of significant was not significant between various bacterial level and several risk factors except for total bacterial count and knowledge about diseases transmitted by raw milk at p < 0.05. It is, therefore, highly recommended that all concerned parties should increase awareness about diseases transmitted by raw milk among milk transporters in Nyagatare district among others.