Familial gastrointestinal stromal tumor (GIST) is a rare autosomal dominant genetic disorder; thus far, only seven families have been reported with c-kit germline mutations. Presented herein is a case of multiple intestinal GIST in a 38-year-old man with a germline mutation of the c-kit gene. Operative specimens of the jejunal segment and multiple wedge resection specimens included approximately 30 masses, ranging in size from 1.0 to 6.0 cm. Microscopically, the tumors were composed of CD117-positive spindle/epitheloid cells with variable numbers of mitotic counts, a characteristic of GIST. The mitotic rate increased to more than 5/50 high-power fields. Interestingly, marked hypertrophy of the myenteric plexus with CD117-positive cells was identified in the intestinal segment. By polymerase chain reaction-single-strand conformation polymorphism analysis and direct DNA sequencing, a heterozygous c-kit missense mutation at nucleotide 1676 of codon 559 (T --> C, Val --> Ala), part of the juxtamembrane domain, was detected in the normal tissue. The same mutation was homozygous in the tumor samples. The present case is the first proven case of multiple GIST with a c-kit germline mutation in Korea and is distinguishable from other reported germ-line c-kit mutations because the same 1676 T --> C missense mutation occurs in the normal allele as well as the affected allele, although the significance of the identical mutations remains to be investigated.