Self-assembling processes of amphiphilic lipids in water give rise to complex architectures known as lyotropic liquid crystalline (LLC) phases. Particularly, bicontinuous cubic and hexagonal LLC phases can be dispersed in water forming colloidal nanoparticles respectively known as cubosomes and hexosomes. These non-lamellar LLC dispersions are of particular interest for pharmaceutical and biomedical applications as they are potentially non-toxic, chemically stable, and biocompatible, also allowing encapsulation of large amounts of drugs. Furthermore, conjugation of specific moieties enables their targeting, increasing therapeutic efficacies and reducing side effects by avoiding exposure of healthy tissues. In addition, as they can be easy loaded or functionalized with both hydrophobic and hydrophilic imaging probes, cubosomes and hexosomes can be used for the engineering of multifunctional/theranostic nanoplatforms. This review outlines recent advances in the applications of cubosomes and hexosomes for in vitro and in vivo bioimaging.