METHODS AND PRINCIPAL FINDINGS: A total of 3776 stool cups was distributed to 26 schools throughout the country. 1760 (46.61%) responded. The overall prevalence of intestinal parasitic infection in both rural and urban areas was 13.3%, with Blastocystis sp (10.6%) being the most predominant, followed by Trichuris trichiura (3.4%), Ascaris lumbricoides (1.5%) and hook worm infection (0.9%). Only rural school children had helminthic infection. In general Perak had the highest infection (37.2%, total, n = 317), followed by Selangor (10.4%, total, n = 729), Pahang (8.6%, total, n = 221), Kedah (6.2%, total, n = 195) and Johor (3.4%, total, n = 298). School children from rural schools had higher infection (13.7%, total, n = 922) than urban school children (7.2%, total, n = 838). Subtype (ST) 3 (54.3%) is the most predominant ST with persons infected with only ST1 and ST3 showing symptoms. Blastocystis sp infection significantly associated with low household income, low parent's education and presence of symptoms (p<0.05).
CONCLUSION: It is critical that we institute deworming and treatment to eradicate the parasite especially in rural school children.