We experienced a 16-year-old patient with T-cell acute lymphoblastic leukemia, who had multiple unrelated chromosomal abnormalities in host cells after chemotherapy and cord blood transplantation (CBT). In 7 consecutive cytogenetic studies after CBT, he showed various chromosomal abnormalities including t(1;11)(p32;q23), t(8;21)(q22.2;q22.2), t(6;10)(p21.3;q26), and del(7) (q22q34). His chromosomal abnormalities were unstable and different in each cytogenetic study except del(7)(q22q34). He had neither anemia nor leukopenia, and his thrombocytopenia continuously improved after CBT. He was clinically stable for 2.5 years despite his complex chromosomal abnormalities. The clinical relevance of genetic instabilities in host cells after CBT is unclear, and long-term monitoring with additional cases is needed.