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There is inadequate information on the etiology of diarrhea in severely malnourished (SM) young children. Thus, the study aimed to determine the etiology of diarrhea among severely malnourished (z score < ?3.00 SD) children in rural and urban Bangladesh. From the database (2000-2011) of Diarrheal Disease Surveillance Systems (DDSS) at rural Matlab and urban Dhaka hospitals of icddr,b, 2234 and 3109 under-5 children were found severely malnourished (underweight, stunted or wasted) respectively. Two comparison groups [moderately malnourished (MM) and well-nourished (WN)] were randomly selected in a ratio of 1:1:1. Children with all categories of SM were more likely to be infected with Vibrio cholerae (rural—11%; urban—15%), Shigella (16%; 9%), Salmonella (1%; 2%) and Campylobacter (3%; 4%); and less likely to have rotavirus (25%; 20%) compared to only one SM category. Isolation rate of Vibrio cholerae was significantly higher among SM both in rural and urban children (7%; 13%) than those of MM (5%; 10%) and WN (2%; 8%) and lower for rotavirus (30%; 31%), (34%; 43%), (35%; 47%) respectively (p < 0.01). However, for Shigella it was only higher among rural SM children (11%) [MM (9%), and WN (8%) (p < 0.01)]. The isolation rate of Salmonella in SM (2%) was similar to that in MM (2%; p = 0.72) but significantly higher than that in WN (1%; p < 0.01) among urban children. Isolation rates of bacterial enteric pathogens were higher but rotavirus was lower in SM children in both rural and urban area with geographical heterogeneity.