Bacterial microcompartments, such as carboxysomes, are primitive organelles composed entirely of protein. They sequester certain enzymatic reactions that would be either inhibited by or toxic to cytoplasmic conditions. The architectural similarity of these compartments to viruses is obvious both in their microscopic appearance and in their underlying design, self-assembling from multiple copies of a few highly similar proteins. Genomic sequence data reveal the presence of microcompartment genes in numerous microbes, indicating that these primitive organelles are more common than previously thought. The prototypical bacterial microcompartment is the carboxysome, a molecular module that optimizes carbon fixation by encapsulating the enzyme RuBisCO in a microenvironment rich in CO2. Our crystallographic studies on carboxysomes found in cyanobacteria and chemoautotrophs provide the first structural insights into carboxysome assembly and function. These data provide a deeper understanding of CO2 fixation in the biosphere as well as illustrate an alternate, perhaps more primitive strategy for biological compartmentalization that can be used to inform the design of optimized and/or novel microcompartments.