Qualitative alterations or abnormal expression of microRNAs (miRNAs) in colorectal cancer have mainly been demonstrated in primary tumors. The miRNA expression profiles in 78 samples from 46 patients were analysed to identify changes in miRNA expression level among normal colon mucosa, primary tumor and liver metastasis samples. Using this dataset, we describe the interplay of miRNA groups in regulating pathways that are important for tumor development. Here we describe in details the contents and quality controls for the miRNA expression and clinical data associated with the study published by Pizzini and colleagues in the BMC Genomics in 2013 (Pizzini et al., 2013). Data are deposited in GEO database as GSE35834 series.