Spinal muscular atrophy (SMA) is the leading genetic cause of infant mortality. SMA results from loss of survival motor neuron (SMN) expression and subsequent death of motor neuron cells. To study SMN-associated proteins that may be involved in transcriptional regulation, we carried out immunoprecipitation experiments and found that the transcription corepressor mSin3A associates with SMN protein. Deletional analysis localized the mSin3A-interacting domain to the exon 6 region of SMN. When targeted to a promoter, wild-type SMN was able to repress transcription of a downstream luciferase reporter gene. This repression was relieved by treatment with the histone deacetylase inhibitor trichostatin A in a dose-dependent manner, and deletion of exon 6 abolished the ability of SMN to repress the reporter gene. Analysis of SMN missense mutations within the exon 6 region implicated the SMA-associated mutation Y272C with impairment of the mSin3A-interaction. Gel filtration experiments revealed that wild-type SMN, via the exon 6 region, forms protein supra-complexes exceeding 40,000 kDa in size, whereas the Y272C mutation may affect higher order protein assembly, as the mutant SMN was more abundant in smaller complexes. Together, these findings provide a potential mechanism by which lack of fully functional SMN protein is detrimental to motor neuron survival.