In this research the factors affecting on the removal of coliform group by certified structure type small-scale Johkasou were analyzed. Before chlorination process, the relevance ratios of effluent standard of the number of coliform group in BOD removal type Johkasou and Nitrogen removal type Johkasou were 70.0% and 88.3%, respectively. The number of coliform group was decreased with the decrease of BOD and SS. Furthermore, the number of coliform group was decreased with the increase of nitrification ratio. After chlorination process, the relevance ratios of effluent standard of the coliform group in BOD removal type Johkasou and Nitrogen removal type Johkasou were 85.0% and 100.0%, respectively. It was also revealed that some small-scale Johkasou, in which the residual chlorine was detected but free chlorine was not detected, could not achieve the effluent standard of coliform group. This is because that combined chlorine was generated by ammonia remained in treated water and the effect of chlorination was reduced to remove coliform group. From these results, it was concluded that certified structure type small-scale Johkasou, especially Nitrogen removal type Johkasou can removal coliform group effectively and contribute to keep hygienic safety.