Ischemic renal injury can produce chronic renal inflammation and fibrosis. This study tested whether ischemia/reperfusion (I/R) activates histone- modifying enzyme systems and alters histone expression at selected pro-inflammatory / pro-fibrotic genes. CD-1 mice were subjected to 30 min of unilateral I/R. Contralateral kidneys served as controls. At 1, 3 or 7 days of reflow, bilateral nephrectomy was performed. Renal cortices were probed for MCP-1, TGF-1, and collagen III mRNAs and cytokine levels. RNA polymerase II (Pol II) binding, which initiates transcription, was quantified at exon 1 of the MCP-1, TGF-1, collagen III genes (chromatin immunoprecipitation assay). Two representative 'gene activating' histone modifications (H3K4m3; histone variant H2A.Z) were sought. Degrees of binding of two relevant histone- modifying enzymes (Set1, BRG1) to target genes were assessed. Renal cortical Set1, BRG1, and H2A.Z mRNAs were measured. Finally, the potential utility of urinary mRNA concentrations as non invasive markers of these in vivo processes was tested. I/R caused progressive increases in Pol II binding to MCP-1, TGF-1, and collagen III genes. Parallel increases in cognate mRNAs also were expressed. Progressive increases in renal cortical Set1, BRG1, H2A.Z mRNAs, and increased Set1 / BRG1 binding to target genes occurred. These changes corresponded with: i) progressive elevations of H3K4m3 and H2A.Z at each test gene; ii) increases in renal cortical TGF-1 / MCP-1 cytokines; and iii) renal collagen deposition (assessed by histo-morphology). Post ischemic increases in urinary TGF-1, MCP-1, Set1, and BRG1 mRNAs were also observed. We conclude that: i) I/R up-regulates histone modifying enzyme systems; ii) histone modifications at pro-inflammatory/pro-fibrotic genes can result; and iii) urinary mRNA assessments may have utility for non invasive monitoring of these in vivo events.