Among infants and toddlers with chronic frequent loose stool, normal frequent and loose stool (NFLS) is more common than diarrheal illness with dehydration and nutritional deficiency (DIDN). To identify more objective factors for differentiating between NFLS and DIDN is important. The frequency, mucus content, and microbiological findings of stools, as well as diaper dermatitis are not important factors to significantly differentiate the groups. Instead, a failure to gain weight, fever, colic/abdominal pain, gross blood in stool (except allergic proctocolitis), nocturnal stool, and the score of the stool quantity are important factors to significantly differentiate the groups. A failure to gain weight is also observed even in NFLS, which may come from iatrogenic diet manipulation with nutritionally deficient food. The most objective differential factors are nocturnal stool and the score of stool amount (≥7 points/day). The use of these objective factors could lessen parental anxiety and distress, iatrogenic undernutrition of patients, and socioeconomic loss due to improper medical investigations or inappropriate management of NFLS.