A 20-year-old male developed early blistering, poikiloderma, hypohidrosis, alopecia and exocrine pancreatic hypofunction caused by atrophy and fatty replacement of the pancreas. At 5 months of age, he initially presented at the hospital with numerous blisters on his extremities, inguinal and genital area. A biopsy specimen from a vesicular lesion showed a subepidermal bulla. Electron microscopic examinations of a vesicular lesion revealed vacuolar changes of the basal cells without hemidesmosomes. Subsequently, the blisters gradually resolved and healed without scars. At the age of 11, he was admitted for the treatment of cellulitis on his foot and at that time, laboratory examinations detected a decreased level of pancreatic enzymes due to exocrine pancreatic hypofunction. Abdominal ultrasonography and computed tomography (CT) showed the pancreas to be atrophic with fatty replacement. A genetic analysis revealed no mutation in his RECQL4 gene, which is responsible for the pathogenesis of Rothmund-Thomson syndrome (RTS). Although marked blister formation and exocrine pancreatic hypofunction are unusual complications of RTS, this case showed many typical clinical features of RTS. Therefore, this case was considered to be a peculiar variant of RTS.