The question of whether any genetic differences exist between primary and colorectal cancers (CRCs) and their metastatic foci is controversial. To look for genetic aberrations involved in metastasis of CRCs to the liver, we performed subtractive comparative genomic hybridization (CGH) experiments using paired samples from 20 CRC patients with primary tumors and synchronous or metachronous liver metastases. Relatively frequent gains in DNA copy number were detected at 6p, suggesting the presence of one or more metastasis-related genes in the region. Analysis of 11 CRC cell lines using array-based CGH (CGH-array) revealed one 6p candidate gene, CCND3. Quantitative reverse transcriptase-polymerase chain reaction experiments showed that CCND3 was significantly upregulated in liver-metastatic lesions compared with primary lesions (P<0.0152). In addition, immunohistochemical analysis of 120 primary CRC tumors demonstrated that cyclin D3 expression in the region of rolled edge was significantly associated with total recurrence, especially hematogenous recurrence (P=0.0307). The results implied involvement of cyclin D3 in liver metastasis of CRC, and the data may contribute to the development of a novel therapy or diagnostic agent for this currently intractable disease. Our experiments also confirmed the power of subtractive CGH and CGH-array analysis for identifying cancer-related genes.