Neospora caninum is an obligate intracellular parasite, forming cysts that affect many domestic and wild animals, having greater importance in canine and bovine species due neurological and reproductive problems. Canids of the genus Canis are recognized as the only definitive hosts of N. caninum until the moment in which sexual phase occurs multiplication, resulting in the elimination of oocysts in the feces. Toxoplasma gondii is also a coccidian parasite responsible for a zoonotic disease of great importance and occurrence around the world. The asexual developmental stage of T. gondii occurs in mammals and birds, the intermediate hosts, resulting in the formation of cysts and the sexual stage occurs in the small intestine of definitive hosts, which are the felids, occurring oocysts formation. This study aimed to determine the seroprevalence of antibodies against Neospora spp. and Toxoplasma gondii in equids from different regions of Brazil and the isolation and genetic characterization of these parasites from equids tissue. Serology for T. gondii and Neospora spp. was performed in 453 serum samples by Immunofluorescence Antibody Test (IFAT). Of this total, eight (1.75%) samples (seven of donkeys and one of horse) were positive to Neospora spp. antibodies and 129 (28.47%) samples (82 donkeys, 32 horses, 15 mules) were T. gondii seropositive. For the isolation of T. gondii, bioassay was performed in mice. A sample of one donkey (Equus asinus) from Mossoró, RN, was obtained with two of the 20 inoculated mouse infected. The mouse died at day 16 th and 17 th post inoculation. The genotypic characterization of the isolate was performed by PCR-RFLP using 12 genotypic markers. Genotyping showed the genotype #60 TgCkBr220, already described in chickens from Fernando de Noronha, PE, Brazil. Due the impossibility of acquisition of tissue from Neospora spp seropositive equids, isolation of this coccidian by gerbil bioassay was not possible to be done.