Interactions between neoplastic cells and neighboring stromal cells affect tumor morphology and behavior. The present study aimed to identify specific chromosomal aberrations that influence tumor-stroma interactions in colorectal cancer (CRC). Chromosome copy number changes of 23 carcinomas were analyzed by comparative genomic hybridization (array-CGH). Stroma percentage was determined by quantitative measurements of hematoxylin-eosin stained sections. Loss of 1p36 was associated with a decrease, and loss of 9q34 with an increase in CRC stroma percentage. Moreover, gain of 8q24 was associated with increased stroma percentage in CRCs with 20q gain, a major event in colon adenoma-to-carcinoma progression. These data indicate that different cancer genomes have different effects on tumor-stroma interactions, and suggest that determination of specific chromosomal aberrations in CRCs may be used as clinical parameter to predict tumor behavior.