Through computer simulation of images produced by the transmission electron microscope (TEM), we have identified three-dimensional periodic cubic membrane structures in giant amoebae (Chaos carolinensis) mitochondria. The cubic membranes are based on the highly curved three-dimensional periodic cubic surfaces, sharing the same geometry of mathematically defined periodic minimal surfaces. The double-membrane structures identified here divide space into three separate and convoluted subspaces. Specimen preparation, specifically the tendency to cut oblique sections, of this membrane crystal has added to the complexity of the resulting TEM projections and until now prevented researchers from recognizing them. It is the added complexity of the oblique sections, though, that allows us to match the TEM projection to a computer simulation of the same with confidence. In this study, formation of cubic membrane structures in amoeba mitochondria was found to be dependent on diet. The cubic structures only occurred in the absence of food, and disappeared in the presence of food, suggesting a structural adaptation and possible advantages for amoeba's survival in nature. The verification of mathematically well-defined structures in unfed amoeba mitochondria is also important to the understanding of the mitochondrial bioenergetics in relation to the topology of the inner membrane, where major cellular energy production as well as free-radical generation are taking place. This understanding may carry great impact upon human health as far as aging and age-related degenerative diseases are concerned, especially as mitochondrial disorders have been implicated in these processes.