Equine piroplasmosis (EP), a reportable disease in Malaysia, caused by Theileria equi, Babesia caballi and both protozoa can result in petechial hemorrhages, hemoglobinuria, and death in equids. The epidemiology of the disease in Malaysia has not been thoroughly investigated. The objectives of this study were to: identify the etiology of EP in Kelantan; determine the prevalence and risk factors; compare the effectiveness of laboratory tests for detecting the disease; identify ticks species on the equids; determine the clinicopathological parameters and antibody titers in equids with a clinical and subclinical form; and investigate the genetic diversity and phylogenetic of the piroplasms from equids and ticks. From September 2013 to March 2014, 53 stables were conveniently selected in eight regions in Kelantan. A total of 306 equids were randomly selected from the stables. Blood, serum and ticks were collected from the equids. Blood smear was stained with Giemsa and examined for T. equi and B. caballi microscopically. Blood was subjected for multiplex PCR to detect T. equi and B. caballi DNA. Blood were also subjected for hematology. Serum was subjected for cELISA to detect antibodies against the protozoa, and also for serum biochemistry. Ticks were identified using taxonomic keys. Epidemiological data were collected through interviews with the stables owners. The 18S rRNA gene of T. equi and B. caballi extracted from blood and ticks were analyzed for genetic diversity and phylogenetic tree using online NCBI BLAST, ClustalX (NCBI) and Neighbor-joining (NJ) programs. Various shapes, sizes, stages and parasitemia level of T. equi and B. caballi were seen in the blood smears. The overall prevalence of EP was 32.02%, 80.06% and 35.62% using microscopic examination, cELISA and multiplex PCR respectively. The risk factors that were important and significantly associated with higher prevalence of EP in Kelantan include imported equids, presence of ticks on equids and nearby animals and presence of other animals near or in the stable. Six species of Ixodid ticks that are important in spreading EP were identified: Rhipicephalus (Boophilus) microplus, Rh. (Boophilus) annulatus, Rh. bursa, Rh. sanguineus, Haemaphysalis longicornis and Dermacentor marginatus. High level of genetic diversity was detected within 18S rRNA gene of T. equi and B. caballi from equids and Ixodid ticks. In conclusion, EP is endemic in Kelantan and several risk factors and species of ticks important in spreading the protozoa were identified. Tick control program should be conducted in order to prevent the transmission of EP.