Dystrophin is a muscle scaffolding protein that establishes a structural link between the cytoskeleton and the extracellular matrix. Despite the large body of knowledge about the dystrophin gene and its interactions, the functional importance of the large central rod domain remains highly controversial. It is composed of 24 spectrin-like repeats interrupted by four hinges that delineate three sub-domains. We express repeat 1-3 and repeat 20-24 sub-domains, delineated by hinges 1-2 and 3-4 and the single repeats 2 and 23. We determine their lipid-binding properties, thermal and urea stabilities and refolding velocities. By using intrinsic tryptophan fluorescence spectroscopy and size exclusion chromatography, we show that repeat 2 and the repeat 1-3 sub-domain strongly interact with anionic lipids. By contrast, repeat 23 and the repeat 20-24 sub-domain do not interact with lipids. In addition, the repeat 1-3 sub-domain and repeat 2 are dramatically less stable and refold faster than the repeat 20-24 sub-domain and repeat 23. The contrasting properties of the two sub-domains clearly indicate that they make up two units of the rod domain that are not structurally interchangeable, thus providing molecular evidence supporting the observations on the biological function of dystrophin.