BACKGROUND The causative pathogen is rarely identified in the emergency department (ED), since the results of cultures are usually unavailable. As a result, antimicrobial treatment may be overused. The aim of our study was to investigate the pathogens, risk factors of acute gastroenteritis, and predictors of acute bacterial gastroenteritis in the ED. METHODS We conducted a matched case-control study of 627 stool samples and 612 matched pairs. RESULTS Viruses (41.3%) were the leading cause of gastroenteritis, with noroviruses (32.2%) being the most prevalent, followed by bacteria (26.8%) and Giardia lamblia (12.4%). Taking antacids (adjusted odds ratio [aOR] 4.10; 95% confidence interval [CI], 2.57-6.53), household members/classmates with gastroenteritis (aOR 4.69; 95% CI, 2.76-7.96), attending a banquet (aOR 2.29; 95% CI, 1.64-3.20), dining out (aOR 1.70; 95% CI, 1.13-2.54), and eating raw oysters (aOR 3.10; 95% CI, 1.61-5.94) were highly associated with gastroenteritis. Elders (aOR 1.04; 05% CI, 1.02-1.05), those with CRP >10 mg/L (aOR 2.04; 95% CI, 1.15-3.62), or those who were positive for fecal leukocytes (aOR 2.04; 95% CI, 1.15-3.62) or fecal occult blood (aOR 1.97; 95% CI, 1.03-3.77) were more likely to be hospitalized in ED. In addition, presence of fecal leukocytes (time ratio [TR] 1.22; 95% CI, 1.06-1.41), abdominal pain (TR 1.20; 95% CI, 1.07-1.41), and frequency of vomiting (TR 0.79; 95% CI, 0.64-0.98) were significantly associated with the duration of acute gastroenteritis. Presence of fecal leukocytes (aOR 2.08; 95% CI, 1.42-3.05), winter season (aOR 0.45; 95% CI, 0.28-0.74), frequency of diarrhea (aOR 1.69; 95% CI, 1.01-2.83), and eating shrimp or crab (aOR 1.53; 95% CI, 1.05-2.23) were highly associated with bacterial gastroenteritis. The area under the receiver operating characteristic curve of the final model was 0.68 (95% CI, 0.55-0.63). CONCLUSIONS Acute bacterial gastroenteritis was highly associated with season, frequency of diarrhea, frequency of vomiting, and eating shrimp or crab.