Chronic infection with the intracellular parasite Toxoplasma gondii produces an accumulation of cysts in the brain and muscle, causing tissue damage. The cysts in the brain motor regions affect some kinematic locomotion parameters in the host. To localize the brain cysts from Toxoplasma gondii and study the changes in kinematic locomotion in C57BL/6 mice. Female adult C57BL/6 mice were infected orally with 30 ME-49 Toxoplasma gondii cysts. An uninfected group (n = 7) and two infected groups, examined 15 and 40 days postinfection, were used for this study. To evaluate kinematic locomotion, the mice were marked with indelible ink on the iliac crest, hip, knee, ankle, and phalangeal metatarsus of the left and right hindlimbs. At least three recordings were carried out to obtain videos of the left and right hindlimbs. Mice were video recorded at 90 fps at a resolution of 640 × 480 pixels while walking freely in a transparent Plexiglass tunnel. We measured the hindlimb pendular movement and the hindlimb transfer [linear displacement] curves for each step and evaluated them statistically with Fréchet dissimilarity tests. Afterward, the mice were sacrificed, and the brain, heart, skeletal muscle, lung, liver, and kidney were obtained. The different tissues were stained with hematoxylin and eosin for analysis with optical microscopy. Topographic localization of the cysts was made using bregma coordinates for the mouse brain. The cysts were distributed in several brain regions. In one mouse, cyst accumulation occurred in the hippocampus, coinciding with an alteration in foot displacement. The step length was different among the different studied groups.