In the present study, transcript profiling was carried out in liver biopsies from high-yielding dairy cows at week 5 of lactation in order to identify genes and pathways regulated by feeding rumen-protected conjugated linoleic acid (CLA) during the transition period. Analysis of a bovine whole genome microarray revealed a total number of 130 annotated differentially expressed genes (DEGs) in the liver between cows of the CLA group and the control group (filter: P < 0.05 and fold change (FC) >= 1.3 or <= -1.3). The number of DEGs in the liver being up-regulated was markedly higher than that being down-regulated (86 vs. 44). Gene set enrichment analysis revealed that the most enriched biological processes and molecular functions assigned to the 86 up-regulated genes were S-methyltransferase activity, ribonucleoprotein complex biogenesis, homocysteine S-methyltransferase activity, methionine biosynthetic process and spliceosome assembly, while the most enriched biological processes and molecular functions assigned to the 44 down-regulated genes were exopeptidase activity, cytokinesis after mitosis, cytokinesis during cell cycle, protein serine/threonine kinase activity and cytokinesis. The microarray dataset from this study has been deposited in NCBI's Gene Expression Omnibus under the accession number GSE87391. (C) 2016 The Authors. Published by Elsevier Inc.