Although high-dose chemotherapy supported by autologous peripheral blood stem cell transplantation (auto-PBSCT) is the standard approach for younger patients with multiple myeloma, some of them still show a poor prognosis. We attempted to define a high-risk group among 32 patients who received auto-PBSCT between August 2000 and July 2007 in our hospital. In conventional metaphase cytogenetics (G-banding), chromosome abnormalities (CA), hypodiploidy, and 13 or 13q deletion (Gd13) were noted in 27.6, 17.2, and 19.4% of patients, respectively. In a FISH study, del(17p) (Fd17p) and t(4;14) were noted in 12.5 and 9.4% of patients, respectively. Prognostic analyses of patients with these abnormal chromosomes revealed that those with CA, hypodiploidy, Gd13, and t(4;14) showed a poorer survival at 3 years compared to those without them: 42.9 vs. 95.2% (p=0.0072), 25.0 vs. 91.5% (p=0.0056), and 40.0 vs. 91.8% (p=0.0245), 0 vs. 89.3% (p<.0001), respectively. When we defined patients showing at least one of CA, hypodiploidy, Gd13, Fd17p, and t(4;14) as a "high-risk group", they showed a poorer overall (23.9 vs. 106.1 mo., p=0.0011) and progression-free (13.5 vs. 25.6 mo., p=0.0095) survival compared to a non-high-risk group. This study indicated that chromosome analysis has a prognostic value in patients with multiple myeloma receiving auto-PBSCT.