HAP1 is a neural protein and interacts with the Huntington's disease protein huntingtin. There are at least two HAP1 isoforms, HAP1-A and HAP1-B, which have different C-terminal amino acid sequences. Here we report that both HAP1 isoforms associate with a unique cytoplasmic structure in neurons of rat brain. The HAP1-immunoreactive structure appears as an inclusion that is an oval mass of electron-dense material, 0.5-3 microm in diameter, containing many curvilinear or ring-shaped segments, and often containing electron-lucent cores. This structure is very similar to those previously termed the stigmoid body, nematosome, or botrysome. Transfection of cell lines with cDNA encoding HAP1-A, but not HAP1-B, resulted in similar HAP1-immunoreactive inclusions in the cytoplasm, suggesting that HAP1-A is essential to the formation of this structure. Yeast two-hybrid and transfection studies show that both HAP1-A and HAP1-B can self-associate, implying that native HAP1 in the cytoplasmic inclusion may be a heteromultimer of HAP1-A and HAP1-B. Coexpression of HAP1-A and HAP1-B in human embryonic kidney 293 cells demonstrates that the ratio of the expressed HAP1-A to HAP1-B regulates the formation of HAP1-associated inclusions. We propose that HAP1 isoforms are involved in the formation of HAP1-immunoreactive inclusions in the neuronal cytoplasm.