S U M M A R YThe rapidly dividing small intestinal epithelium is very sensitive to the cytostatic drug methotrexate. We investigated the regulation of epithelial gene expression in rat jejunum during methotrexate-induced damage and regeneration. Ten differentiation markers were localized on tissue sections and quantified at mRNA and protein levels relative to control levels. We analyzed correlations in temporal expression patterns between markers. mRNA expression of enterocyte and goblet cell markers decreased significantly during damage for a specific period. Of these, sucrase-isomaltase ( Ϫ 62%) and CPS ( Ϫ 82%) were correlated. Correlations were also found between lactase ( Ϫ 76%) and SGLT1 ( Ϫ 77%) and between I-FABP ( Ϫ 52%) and L-FABP ( Ϫ 45%). Decreases in GLUT5 ( Ϫ 53%), MUC2 ( Ϫ 43%), and TFF3 ( Ϫ 54%) mRNAs occurred independently of any of the other markers. In contrast, lysozyme mRNA present in Paneth cells increased ( ϩ 76%). At the protein level, qualitative and quantitative changes were in agreement with mRNA expression, except for Muc2 ( ϩ 115%) and TFF3 ( ϩ 81%), which increased significantly during damage, following independent patterns. During regeneration, expression of each marker returned to control levels. The enhanced expression of cytoprotective molecules (Muc2, TFF3, lysozyme) during damage represents maintenance of goblet cell and Paneth cell functions, most likely to protect the epithelium. Decreased expression of enterocyte-specific markers represents decreased enterocyte function, of which fatty acid transporters were least affected.