Three to five million children from among one billion with gastroenteritis die annually worldwide. The etiologic agent in developed countries is viral in 15-60% of cases, while in developing countries, bacteria and parasites are frequently reported as the etiologic factors. Neurologic signs including convulsion are seen in some cases of diarrhea. This study aimed to investigate the etiology, risk factors and short-term prognosis of gastroenteritis with convulsion. During a case-control study, 100 patients with gastroenteritis were enrolled into the case and control groups on the basis of convulsion or no convulsion development, respectively. This study was conducted in Tabriz Children's Hospital from March 2004 to March 2007. The age of patients ranged from 2 months to 7 years, and the groups were age- and sex-matched. Body temperature (BT), severity and type of dehydration, stool exam and culture, past history of convulsion in the patient and first-degree relatives, electrolyte imbalance, and short-term prognosis were studied and compared. The mean weight of groups was not different, while the frequency of fever at the time of admission, past history of febrile convulsion in first-degree relatives and severity of dehydration were significantly higher in the case group (p < 0.001). The BT of the case group on admission was higher than in the control group (39.01+/- 0.80 vs. 37.52 +/- 0.67 degrees C; p < 0.001). Past history of febrile convulsion in the patient, shigellosis and antibiotic usage were also significantly higher in the case group (p = 0.025, p = 0.014 and p = 0.001). Convulsion mostly occurred in mild gastroenteritis accompanied with fever and positive history of febrile convulsion in first-degree relatives. History of febrile convulsion in the patient and shigellosis were associated with development of convulsion in patients with gastroenteritis. No significant electrolyte imbalance was observed in patients with gastroenteritis experiencing febrile convulsion.