Enteric coccidiosis may cause significant morbidity and mortality in juvenile brown kiwi (Apteryx mantelli). Morphology of sporulated oocysts indicates that at least two Eimeria species are able to infect the brown kiwi. A histological study of the endogenous stages of coccidia was undertaken in the intestinal tracts of ten naturally infected young kiwi. Sequential sectioning of the entire intestinal tract allowed identification and recording of the distribution of the various coccidial life stages. Macromeronts measuring 268 × 162 μm when mature were found mainly within the lamina propria of the proximal one third of the small intestine. A smaller form of lamina propria meront was also identified (8.7 × 6.4 μm) with a similar distribution to the macromeronts. Small meronts (4.4 × 3.8 μm) were also identified in mucosal epithelial cells, with the overall peak in distribution within the intestinal tract being distal to the lamina propria meronts. Three morphologically distinctive gametocytes were identified. Type A gametocytes contained within epithelial cells shared the same distribution as the epithelial meronts. Polyps containing large numbers of type B gametocytes within the distal intestinal tract were found in two cases, and type C gametocytes were identified throughout the entire intestinal tract in one case only. The observational nature of this study precludes complete knowledge of the parasite life cycles using histology alone. However, it is likely that each of the three morphologically distinct gametocytes represents a separate species of enteric coccidia.