The peripheral muscle membrane protein rapsyn is essential for the formation and maintenance of high density acetylcholine receptor aggregates at the neuromuscular synapse. Rapsyn is concentrated at synaptic sites and is colocalized with acetylcholine receptors from the earliest stages of synaptogenesis. Previous studies have shown that recombinant rapsyn expressed in heterologous cells forms clusters, and acetylcholine receptors coexpressed with rapsyn are colocalized with rapsyn clusters. However, the molecular interactions involved in clustering of rapsyn are not well defined. To analyze the process of cluster formation by rapsyn we examined the formation of rapsyn clusters and complexes using mutant constructs specifically deleted for individual domains of rapsyn in the presence and absence of tagged, full-length rapsyn. Specific deletions of the tetratricopeptide repeat (TPR) domains 1 and 3 of rapsyn abrogated not only clustering of mutant rapsyns, but also, in a dominant negative fashion, the clustering of tagged, full-length rapsyn. We also analyzed rapsyn protein complexes isolated from cells transfected with tagged and untagged rapsyn. Our results show that both tagged and untagged rapsyn are present in immunoprecipitates of rapsyn from cotransfected cells, demonstrating that rapsyn molecules interact directly or indirectly to form oligomers. Mutants that were dominant negatives were also present in complexes containing tagged, full-length rapsyn. Together these results indicate that rapsyn forms clusters at the synapse by oligomerization, and suggest models for the mechanistic bases of this oligomerization via interactions mediated by TPRs 1 and 3.