Microsporidia constitute a large group of obligate intracellular protozoan parasites that inject themselves into host cells via the extrusion apparatus of the infective spore stage. Although the injection process is poorly understood, its energy source is thought to reside in the posterior vacuole that swells significantly during spore firing. Here we report the presence and localisation of the key peroxisomal enzymes catalase and acyl-CoA oxidase (ACOX) within the posterior vacuole of Spraguea lophii (Doflein, 1898) spores. Western blot analyses show that these enzymes discharge out of the spore and end up in the medium external to the extruded sporoplasms. The presence of a catalase enzyme system in the Microsporidia was first made evident by the detection of significant levels of molecular oxygen in the medium containing discharging spores in the presence of hydrogen peroxide. Catalase was visualised in inactive, activated, and discharged spores using alkaline diaminobenzidine (DAB) on glutaraldehyde-fixed cells. The position of these enzymes within the extrusion apparatus before and during spore discharge support the Lom and Vávra model that postulates discharge occurs by an eversion process. In addition to these enzymes, spores of S. lophii contain another characteristic peroxisomal component, the very long chain fatty acid (VLCFA) nervonic acid. A sizeable decrease in nervonic acid levels occurs during and after spore discharge. These data indicate that nervonic acid is discharged from the spore into the external medium during firing along with the catalase and ACOX enzymes.