OBJECTIVE The mouse diarrhea score is usually determined by evaluating stool consistency and shape. Thus, defecated stools should be collected without damage or contamination. The study aimed to develop improved mouse stool collection methods and diarrhea-scoring criteria. METHODS We developed improved stool collection methods (paper towel methods) and compared them with previously used ones (stool collection using regular cages containing bedding chips or filter paper and metabolic cages). RESULTS Compared to previously used methods, paper towel methods collected stools without bedding chips-induced contamination, mouse body/foot-induced damage, or sampling errors. When using paper towel methods, wet stools create water marks (diarrhea marks) on paper towels with strong water absorption capacity, by which diarrheal severity can be analyzed semi-quantitatively. To improve the objectivity in determining diarrhea scores, practical diarrhea-scoring criteria were also proposed. CONCLUSIONS These results would be helpful to researchers facing difficulties in evaluating the mouse diarrhea score.