Between 1993 and 2011, a total of 371 intestinal amebiasis (IA), caused by Entamoeba histolytica cases were compared with 1,113 shigellosis (randomly selected) patients of icddr,b, excluding co-infections (rotavirus and Vibrio cholerae) in two age stratums: 0-14 years of age and ≥ 15 years of age. The number of IA and shigellosis cases gradually reduced over the study period. In multivariate analysis, individuals 0-14 years of age, slum dwellers (odds ratio [OR] 3.51; 95% confidence interval [CI] 1.69-7.24; P < 0.001), red blood cell (0.44 [0.24-0.86] 0.016), fecal leukocytes (0.17 [0.07-0.33] < 0.001), and alkaline stool (0.16 [0.07-0.36] < 0.001) were independently associated with IA; and among individuals ≥ 15 years of age, living in the slum area (1.88 [1.12-3.14] 0.016), watery stool (2.21 [1.37-3.55] 0.001), use of antimicrobials before visiting hospital (0.67 [0.46-0.99] 0.047), red blood cell (0.45 [0.22-0.94] 0.036), and fecal leukocytes (0.21 [0.12-0.35] < 0.001) in stool were independently associated with IA. Socio-demographic and clinical characteristics of IA and shigellosis varied distantly from each other.