Toxoplasma gondii (T. gondii), a zoonotic parasite, can cause severe disease in warm-blooded animals. Pathological changes in murine tissues infected with different T. gondii isolates were studied to establish factors influencing lesion severity and parasite burden. In Study A, mice were orally inoculated with genotype #3, #6 or #8 oocysts. In Study B, mice were inoculated intraperitoneally with genotype #1, #3, #6, #13, #141 or #265 tachyzoites. Mice were euthanised serially and tissues processed for histopathology. In Study A, genotype #6 caused pathology in the liver, brain, lung, intestine and kidney, predominantly associated with tachyzoites, while #8 caused mainly moderate pathology in the brain, lung and liver, usually associated with tissue pseudocysts/cysts. Genotype #3 occasionally caused mild pathology, but the parasite was not visible in examined tissues. In Study B, genotypes #13 and #6 caused systemic infections associated with tachyzoites. Genotypes #3, #141 and #265 caused moderate pathology associated with pseudocysts/cysts in the brain and tachyzoites in peripheral organs. Genotype #1 caused mild pathology associated with pseudocysts/cysts in organs assessed. Comparison of genotype #6 between studies showed parasite stage and inoculation method did not affect the severity of pathology, but for #3, pathology was more severe when mice were inoculated intraperitoneally with tachyzoites compared to those inoculated orally with oocysts. This study confirmed route of infection, T. gondii strain, life stage and dose influence infection outcome and ultimately contributes to the refinement of T. gondii pathogenesis knowledge, which is fundamental for toxoplasmosis management and treatment.