Annually, there are 165 million cases of shigellosis resulting in 1.1 million deaths in the developing world. Two species of the causative agent, Shigella dysenteriae 1 and Shigella flexneri, are responsible for acute diarrheal illness. Vaccines are being developed against both but many questions remain about the disease burden, distribution of species in space and time, and community-level risk factors. This study answers two questions. What are the differences in neighborhood-level risk factors between S. dysenteriae 1 and S. flexneri? Does shigellosis caused by the two different species occur in the same neighborhoods and are those high-risk neighborhoods persistent in time? Cases from a hospital in rural Bangladesh were assigned to one of the two shigellosis types and age-matched individuals were randomly chosen from the community to be controls. Information was collected for neighborhood-level variables hypothesized to be related to shigellosis. During the 3-year study period, there were 161 cases of S. dysenteriae 1 and 225 cases of S. flexneri. Incidence of both types was highest in children under 2 followed by children from 2 to 5. The location of S. dysenteriae 1 risk varies in time but S. flexneri risk areas were persistent in time. Neighborhoods near bazaars with many non-septic latrines were at highest risk for S. dysenteriae 1. S. flexneri was most common in flood-controlled areas. S. dysenteriae 1 risk is more related to hygiene and sanitation and S. flexneri is more related to the environment.