Chromosome instability (CIN) is characterized by an increased rate of the unequal distribution of DNA between daughter cells. These large changes in chromosome structure or number can occur due to both mitotic defects leading to aneuploidy and DNA damage-induced chromosome rearrangements. Previous large-scale screens for CIN genes identified DIS3, which codes for a catalytic component of the core RNA exosome complex, as a novel CIN gene in the yeast Saccharomyces cerevisiae. Presumed reduction-of-function mutations in the human DIS3 orthologue have been identified in roughly 11% of multiple myeloma (MM) cases. We sought to determine the mechanism of CIN in DIS3 mutants and to recapitulate MM-associated point mutations at conserved sites in yeast cells, in order to understand potential connections of CIN to MM. We have found that MM-associated DIS3 mutations induce DNA:RNA hybrid accumulation and increased rate of CIN, although immunofluorescence analysis of DNA damage foci revealed no increase in double-strand breaks. Microarray analysis of one MM mutant has additionally demonstrated downregulation of cell cycle components, consistent with the potential for mitotic defects. Further, genetic interaction profiling by synthetic genetic array indicates MM-associated DIS3 mutations synthetically interact with rRNA processing proteins, as well as a host of mitotic regulators and metabolic pathways. Together, these results demonstrate extensive phenotypic consequences of MM-associated point mutations in DIS3, and support a model for CIN in DIS3 mutants involving defects in cell cycle processes.