BACKGROUND: Cholera and shigellosis are endemic on the Indian subcontinent. Our objective was to identify cholera-specific risk factors distinct from shigellosis risk factors. METHODS: We conducted a case-case study among hospitalized diarrheal patients, comparing those with cholera and shigellosis in International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) hospitals in Matlab (rural) and Dhaka (urban) between January 1, 2000 and December 31, 2008. RESULTS: Multivariable Poisson regression models revealed that having more than nine years of education, compared to no education, was associated with a 39% (adjusted Risk Ratio [aRR] = 0.61, 95% confidence interval [CI]: 0.40-0.93) decreased risk for cholera hospitalization in Matlab and a 16% (aRR = 0.84, 95% CI: 0.75-0.94) decreased risk in Dhaka. Having a family member with diarrhea in the past seven days increased cholera hospitalization risk by 17% (aRR = 1.17, 95% CI: 1.09-1.26) in Matlab. CONCLUSIONS: Further studies are needed to elucidate the pathway through which education impacts cholera risk in order to create targeted interventions in cholera-endemic areas. Interventions seeking to reduce transmission and facilitate hygienic practices among family members of index cases with diarrhea should be considered, especially in rural cholera endemic settings.