Shwachman-Diamond syndrome (SDS) is a genetic disorder characterized by pancreatic hypoplasia, recurrent infection, and bone marrow (BM) dysfunction. SDS-patients have an increased frequency of myelodysplasia and leukemic transformation. Unspecific cytogenetic aberrations are a common finding in SDS. However, in a rising number of patients abnormalities of chromosome 7 have been reported, especially an i(7)(q10), which seems to be a non-random chromosome abnormality. Recently, the SDS gene has been mapped at locus 7q11 and subsequently cloned; recurrent mutations have been found. We report a case of SDS with an i(7)(q10) in the BM and two different mutations in the SBDS gene. At the age of 25 years, the patient suffers from mild aplastic anemia but does not show any clinical sign of myelodysplasia or leukemic transformation.