A hydrogenosome is a hydrogen-producing organelle, evolutionary related to mitochondria and is found in Parabasalia protozoa, certain chytrid fungi and certain ciliates. It displays similarities to and differences from mitochondria. Hydrogenosomes are spherical or slightly elongated organelles, although very elongated hydrogenosomes are also found. They measure from 200 nm to 1 microm, but under stress conditions can reach up to 2 microm. Hydrogenosomes are surrounded by two closely apposed membranes and present a granular matrix. Cardiolipin has been detected in their membranes, and frataxin, which is a conserved mitochondrial protein involved in iron metabolism, was also recently found. Hydrogenosomes have one or multiple peripheral vesicles, which incorporate calcium. The peripheral vesicle can be isolated from the hydrogenosomal matrix and can be considered as a distinct hydrogenosomal compartment. Dysfunctional hydrogenosomes can be removed by an autophagic process and further digested by lysosomes. Hydrogenosomes divide in three different ways, like mitochondria, by segmentation, partition and the heart form. They may divide at any phase of the cell cycle. Nucleoid or electron dense deposits found in hydrogenosomes can be considered artifacts or dysfunctional hydrogenosomes. The hydrogenosome does not contain a genome, although DNA has already been detected in one anaerobic ciliate. Hydrogenosomes can be considered as good drug targets since their metabolism is distinct from mitochondria.