Background: While traditional models of Alzheimer's disease focused on large fibrillar deposits of the A beta(42) amyloid peptide in the brain, recent work suggests that the major pathogenic effects may be attributed to SDS-stable oligomers of A beta(42). These A beta(42) oligomers represent a rational target for therapeutic intervention, yet factors governing their assembly are poorly understood. Results: We describe a new yeast model system focused on the initial stages of A beta(42) oligomerization. We show that the activity of a fusion of A beta(42) to a reporter protein is compromised in yeast by the formation of SDS- stable low-n oligomers. These oligomers are reminiscent of the low-n oligomers formed by the A beta(42) peptide in vitro, in mammalian cell culture, and in the human brain. Point mutations previously shown to inhibit A beta(42) aggregation in vitro, were made in the A beta(42) portion of the fusion protein. These mutations both inhibited oligomerization and restored activity to the fusion protein. Using this model system, we found that oligomerization of the fusion protein is stimulated by millimolar concentrations of the yeast prion curing agent guanidine. Surprisingly, deletion of the chaperone Hsp104 (a known target for guanidine) inhibited oligomerization of the fusion protein. Furthermore, we demonstrate that Hsp104 interacts with the A beta(42)-fusion protein and appears to protect it from disaggregation and degradation. Conclusion: Previous models of Alzheimer's disease focused on unravelling compounds that inhibit fibrillization of A beta(42), i.e. the last step of A beta(42) assembly. However, inhibition of fibrillization may lead to the accumulation of toxic oligomers of A beta(42). The model described here can be used to search for and test proteinacious or chemical compounds for their ability to interfere with the initial steps of A beta(42) oligomerization. Our findings suggest that yeast contain guanidine-sensitive factor(s) that reduce the amount of low-n oligomers of A beta(42). As many yeast proteins have human homologs, identification of these factors may help to uncover homologous proteins that affect A beta(42) oligomerization in mammals. Conclusion: Previous models of Alzheimer's disease focused on unravelling compounds that inhibit fibrillization of A beta(42), i.e. the last step of A beta(42) assembly. However, inhibition of fibrillization may lead to the accumulation of toxic oligomers of A beta(42). The model described here can be used to search for and test proteinacious or chemical compounds for their ability to interfere with the initial steps of A beta(42) oligomerization. Our findings suggest that yeast contain guanidine-sensitive factor(s) that reduce the amount of low-n oligomers of A beta(42). As many yeast proteins have human homologs, identification of these factors may help to uncover homologous proteins that affect A beta(42) oligomerization in mammals.