Coccidiosis is a major intestinal parasitic disease of poultry that is associated with severe economic losses and welfare issues. This review brings together current knowledge about the disease and the pathological alterations involved at gross, microscopic and molecular level and how these aspects may be exploitable in the future to improve existing control measures. Particular attention was paid to the genotoxic and cytotoxic effects of Coccidia at the cellular level, and how these can be investigated using novel techniques, such as the single-gel electrophoresis (comet assay) on in vitro cultured cells.