The protein Pcf11 has been shown to dismantle RNA polymerase II elongation complexes and has been implicated in transcription termination in yeast, Drosophila and human cells. To obtain more insight into the termination process, I analyzed the distribution of Pol II in Drosophila cells at the 3’ end of three heat shock genes using permanganate genomic footprinting and at the 3’ end of all genes using ChIP-chip. The high resolution footprinting analysis at the 3’ end of the heat shock genes identified several regions where Pol II accumulates. The changes in Pol II distribution at the 3’ end of all three heat shock genes and more than 2000 other genes upon depletion of Pcf11 reveal defects in termination, indicating that Pcf11 functions as a general termination factor. In addition, there are changes in the Pol II distribution at the 5’ end of genes that indicate Pcf11 broadly impacts the behavior of Pol II as might be expected for a protein required for recycling Pol II. My analysis also identified a collection of genes whose transcription might be controlled by Pcf11-dependent premature termination. Three distinct distributions of Pol II are observed at the 3’ end of genes, suggesting the existence of alternative termination mechanisms. Finally, there is a striking decrease in the density of Pol II at the polyadenylation site that correlates with the paucity of nucleosomes in this region. Thus chromatin structure appears to impact the behavior of Pol II at the 3’ end of genes.