Congenital sucrase-isomaltase deficiency (CSID) is a rare autosomal carbohydrate malabsorption disorder caused by mutations in the sucrase-isomaltase gene. While the prevalence of CSID is high in the indigenous populations of Alaska and Greenland, it is imprecise and ambiguous in the Turkish pediatric population. In this cross-sectional case-control study, which is retrospective in nature, next-generation sequencing (NGS) results obtained from records of 94 pediatric patients with chronic nonspecific diarrhea were reviewed. Demographic characteristics, clinical symptoms and treatment responses of those diagnosed with CSID were evaluated. We identified one new, homozygous frame-shift mutation and 10 other heterozygous mutations. Two cases were from the same family and nine were from different families. While the median age at onset of symptoms was 6 months (0-12), median age at diagnosis was 60 months (18-192) with a median delay of 5 years and 5 months (10 months -15 years and 5 months) in diagnosis. Clinical symptoms included diarrhea (100%), abdominal pain (54.5%), vomiting after consuming sucrose (27.2%), diaper dermatitis (36.3%) and growth retardation (81%). Our clinical study revealed that sucrase-isomaltase deficiency may have been underdiagnosed in patients with chronic diarrhea in Turkey. In addition, the frequency of heterozygous mutation carriers was significantly higher than that of homozygous mutation carriers and those with a heterozygous mutations responded well to the treatment.