Abstract: Paf1 is an RNA polymerase II-associated protein in yeast, which defines a complex that is distinct from the Srb/Mediator holoenzyme. The Paf1 complex, which also contains Ctr9, Cdc73, Hpr1, Ccr4, Rtf1 and Leo1, is required for full expression of a subset of yeast genes, particularly those responsive to signals from the Pkc1/MAP kinase cascade. We have extensively characterized the pleiotropic phenotypes of deletion mutants for factors present in the Paf1 complex, identifying more than a dozen new phenotypes, and, in some cases, establishing possible molecular explanations for the growth defects. For example, paf1 Delta causes sensitivity to hydroxyurea; this phenotype correlates with a reduction in RNR1 transcript abundance and is suppressed by over-expression of RNR1. In contrast, the resistance of paf1 Delta cells to the transcription elongation inhibitors 6-azauracil and mycophenolic acid correlates with its ability to derepress the IMD2 transcript. We tested the hypothesis that Paf1 communicates with some promoters through the DNA-binding factors Swi4, Mbp1 or Rlm1. The phenotypes of mutations in Paf1 complex components are exacerbated in the swi4 Delta background, suggesting that the complex acts in a pathway parallel to that controlled by Swi4. Conversely, the fact that mbp1 Delta and rlm1 Delta mutations do not enhance the phenotypes suggests that the Paf1 complex may function in the same regulatory pathway(s) with Mbp1 and Rlm1.