Nonlamellar lyotropic liquid crystalline (LLC) nanoparticles are a family of versatile nano-self-assemblies, which are finding increasing applications in drug solubilization and targeted drug delivery. LLC nanodispersions are heterogeneous with discrete nanoparticle subpopulations of distinct internal architecture and morphology, frequently coexisting with micelles and/or vesicles. Diversity in the internal architectural repertoire of LLC nanodispersions grants versatility in drug solubilization, encapsulation, and release rate. However, drug incorporation contributes to the heterogeneity of LLC nanodispersions, and on exposure to biological media, LLC nanodispersions often undergo nanostructural and morphological transformations. From a pharmaceutical perspective, coexistence of multiple types of nanoparticles with diverse structural attributes, together with media-driven transformations in colloidal characteristics, brings challenges in dissecting biological and therapeutic performance of LLC nanodispersions in a spatiotemporal manner. Here, we outline innate and acquired heterogeneity of LLC nanodispersions and discuss technological developments and alternative approaches needed to improve homogeneity of LLC formulations for drug delivery applications.