A survey of the molecular features of microsporidia is presented which attempts to comment on unresolved questions concerning the physiology of these amitochondrial intracellular parasites. Various transports of host-derived molecules can be predicted and trehalose appears as a potential reserve of glucose for energy metabolism. Significant insights into membrane lipids, polyamine metabolism and sporogony-specific proteins have been gained. Some species, such as Encephalitozoon cuniculi, are heterogeneous entities and harbor a small genome. Although showing a variation in genome size of 8.5-fold, microsporidia share reduced rDNA genes. Finally, data on gene organization and a possible evolutionary relationship with fungi are considered.