High levels of transcription driven by the GAL1-10 promoter stimulate mitotic recombination between direct repeats (DR) as well as between substrates positioned on non-homologous chromosomes. When the substrates are on non-homologous chromosomes, transcription stimulates both gene conversion and crossover events, but the degree of the stimulation varies depending on which substrate is highly transcribed. In gene conversion assays where only one of the substrates is highly transcribed, the effect of transcribing the donor versus the recipient allele can be highly asymmetric. We have examined the basis of this asymmetry and demonstrate that it relates to the nature of the mismatch present in recombination intermediates and the presence of the Msh3 mismatch repair (MMR) protein. In addition to examining the asymmetry conferred by donor versus recipient allele transcription, the possible contribution of transcription elongation problems to transcription-stimulated recombination has been examined using hpr1 mutants. Hpr1 is important for efficient elongation through certain sequences, and in hpr1 mutants, elongation problems have been correlated with elevated recombination between direct repeats. As expected, we found that combining loss of Hpr1 with high levels of transcription had very strong synergistic effects on recombination rates between direct repeats. When the substrates were on non-homologous chromosomes, a weaker synergistic interaction between transcription and Hpr1 loss was observed in gene conversion assays, but only an additive relationship was observed in a crossover-specific assay. Although these data support a causal link between transcription elongation problems and elevated recombination rates, they also indicate that high levels of transcription can stimulate recombination by additional mechanisms.