Toxoplasma gondii, Neospora caninum and Sarcocystis spp. are parasites detected in tissues of domestic and wild animals. Birds are relevant in the life cycle and epidemiology of protozoa due to the wide variety of bird species, feeding and migratory habits. The aim of this study was the molecular detection of T. gondii, N. caninum and Sarcocystis spp. in several species of naturally infected birds. Therefore, samples of brain and heart tissue were collected from birds received and necropsied at the Central Laboratory for the Diagnosis of Avian Pathologies (LCDPA), undergoing DNA extraction and amplification by the polymerase chain reaction (PCR) of the 18S rRNA gene to Sarcocystis spp., NC5 gene for N. caninum and repetitive gene 529 base pairs for T. gondii. N. caninum was detected in two birds (02/65, 3.07%), in a brain sample of Rupornis magnisrostris (accession number: ON182081, 267pb) and in a brain and heart sample of Dendrocygna bicolor (accession number: ON211312, 267pb). DNA of the genus Sarcocystis was detected in three birds (03/65, 4.62%), and in the genetic sequencing Sarcocystis spp. (accession number: MW463929) in brain of Nymphicus hollandicus and Sarcocystis speeri (accession number: MW464125) in brain and heart of Amazona aestiva. Phylogenetic analysis revealed that Sarcocystis spp. formed a clade with Sarcocystis spp. that use skunk (Didelphis aurita) as definitive host and Sarcocystis falcatula that use Moluccan loris (Trichoglossus moluccanus) as intermediate host. S. speeri formed a clade with S. speeri that used Mus musculus as an experimental intermediate host and formed a clade with Sarcocystis columbae, Sarcocystis corvusi, Sarcocystis halieti and Sarcocystis sp. that affect bird species. T. gondii DNA was not detected in any tissue. This is the first report of DNA detection of N. caninum, Sarcocystis spp. and S. speeri in tissue samples for these bird species extending the list of intermediate hosts.