Epithelial cell cultures, including immortalized cells, have been used extensively to help answer basic questions of mammary gland physiology under normal or diseased conditions. The usefulness of using cell culture depends on the degree of identify compared to the in vivo mammary epithelium. Our objective was to compare the transcriptome by means of microarray and qPCR of immortalized bovine mammary epithelial cells (Mac-T) cultivated in plastic (i.e., 2 dimensional system) vs. mammary tissue obtained during late-pregnancy (-30 DIM) and peak lactation (+60 DIM). Functional analysis of microarray data was performed using enrichment analysis tools and the Dynamic Impact Approach (DIA). Overall, between 37% (vs. +60 DIM) and 44% (vs. -30 DIM) of the measured annotated genes were deemed as differentially expressed (DEG) between Mac-T cells and mammary tissue. These data, together with the bioinformatics results of the genes non-differentially expressed, indicated a larger overall similarity between Mac-T cells and lactating than non-lactating mammary tissue. However, Mac-T cells had a lower expression measured by qPCR of genes involved in milk synthesis compared to mammary tissue. The functional analysis of DEG further supported the poor lactation phenotype of Mac-T cells compared with mammary tissue. The bioinformatics analyses of DEG suggested that Mac-T cells cultivated on plastic had greater reliance on glucose, amino acids, and fatty acids for production of energy, greater cell-to-cell interactions, and more prone to react to inflammatory mediators relative to mammary tissue. Despites these differences, data suggest that Mac-T cells might be adequate for studying milk protein regulation. For studies of milk fat regulation Mac-T cells might be not as sensitive as the mammary tissue, particularly for its lower expression of PPARG and lower induction of PPARγ- and LXR-related pathways. Overall, this study revealed a marked difference in the transcriptome signatures between mammary tissue and Mac-T cells cultivated on plastic.