Intranuclear rodlets (INRs), also known as rodlets of Roncoroni, are poorly understood intranuclear bodies originally identified within neuronal nuclei on the basis of their unique morphology. The mechanisms of their formation, their biochemical composition and their physiological significance remain unknown. Using double immunofluorescence staining of mouse brain sections, we identified a novel variant of INR that is immunoreactive for the 40 kDa huntingtin associated protein (Hap40) and ubiquitin, and provide evidence for the existence of additional INR subtypes sharing ubiquitin immunoreactivity as a common feature. We describe a selective association of these INRs with melanin concentrating hormone (MCH) and tyrosine hydroxylase immunoreactive neurons of the hypothalamus and the locus coeruleus, respectively. We also demonstrate for the first time that biochemically distinct INR subtypes can coexist within a single nucleus where they engage in nonrandom spatial interactions. Our findings highlight the biochemical diversity and cell type-specific expression of these enigmatic intranuclear structures. J. Comp. Neurol. 521:3832–3846, 2013. © 2013 Wiley Periodicals, Inc.