The present study aimed to identify microRNA (miRNA) expression profiles associated with brain metastases of colorectal cancers. We conducted miRNA expression profiling of 3 primary colorectal cancers and 3 brain-metastatic carcinomas using Agilent Human miRNA Microarrays. Quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR) was employed to validate the results obtained from the miRNA microarray analysis. Overexpression of miR-145, miR-1, miR-146a, miR-576-5p, miR-126*, HS287, miR-28-5p, miR-143, miR-199b-5p, miR-199a-5p, miR-10b, miR-22, miR-133b, miR-145*, miR-199a, miR-133a, miR-125b and downregulation of miR-31 and HS170 were observed in brain-metastatic carcinomas. Quantitative RT-PCR experiments with miR-125b confirmed the expression patterns we found in our microarray experiments. miRNAs are differentially expressed between colorectal cancers and matched brain-metastatic carcinomas. The miRNA variation trend is quite different in the process of metastasis compared to that of carcinogenesis. These miRNAs may therefore serve as potential diagnostic markers and therapeutic targets for colorectal cancers with brain metastases.