Regulation of gene expression by stress-activated protein kinases (SAPKs) is essential for cell adaptation to extracellular stimuli. Exposure of yeast to high osmolarity results in activation of the SAPK Hog1, which associates with transcription factors bound at target promoters and stimulates transcriptional initiation. Unexpectedly, activated Hog1 also associates with elongating Pol II and components of the elongation complex. Hog1 is selectively recruited to the entire coding region of osmotic stress genes, but not to constitutively expressed genes. Selective association of Hog1 with the transcribed region of osmoresponsive genes is determined by the 3' untranslated region (3' UTR). Lastly, Hog1 is important for the amount of the RNA polymerase II (Pol II) elongation complex and of mRNA produced from genes containing osmoresponsive coding regions. Thus, in addition to its various functions during transcriptional initiation, Hog1 behaves as a transcriptional elongation factor that is selective for genes induced upon osmotic stress.