Nuclear aggregates of enhanced green fluorescent protein and nuclear localization signal-fused truncated N-terminal huntingtin containing 150 repeats of glutamine residue were purified from ecdysine-inducible mutant neuro2A cell line by sequential extraction of nuclear soluble proteins. To analyze the aggregate-interacting proteins, we subjected the nuclear aggregates to high performance liquid chromatography-mass spectrometry analysis. The resulting data revealed the presence of three new putative aggregate-interacting proteins: ubiquilin 1, ubiquilin 2 and Tollip. These proteins also associated with neuronal intranuclear inclusions in a mouse model of Huntington disease (HD). These aggregate-interacting proteins contain ubiquitin-interacting motifs, suggesting that they are recruited to the aggregates where they may lose their normal function.