Molecular genetics studies are of increasing importance in the diagnosis and classification of congenital diarrheal disorders. We describe the molecular genetic basis of tricho-hepato-enteric syndrome in patients from Saudi Arabia with novel mutations of SKIV2L (c.3559_3579del, p.1187_1193del) and TTC37 (C4102T, p.Q1368X). Interestingly, the congenital presence of café-au-lait spots and their distribution in the pelvis and lower limbs were a unique and consistent clinical feature of these patients and may aid differential diagnosis of congenital diarrheal disorders. This study expands allelic and phenotypic heterogeneity of syndromic diarrhea/tricho-hepato-enteric syndrome.