An 8-year-old male with lymphoblastic lymphoma was noted to have multiple café-au-lait macules and possible Lisch nodules. Work-up revealed the child as compound heterozygous for mutations in the DNA mismatch repair gene, MSH6. This case emphasizes many clinical issues regarding individuals with biallelic mismatch repair mutations, a rare and easily missed hereditary predisposition to childhood cancer. The issues include the need for high clinical suspicion based on skin examination findings and family history, the phenotypic similarity to neurofibromatosis type 1 with possibility of misdiagnosis, the high risk for subsequent malignances, and the need for further research of possible treatment resistance.