Objective: To determine the true prevalence of soil-transmitted helminth infections in the Malaysian aborigines using real-time PCR. Methods: A total of 122 aborigines from seven tribes were recruited from settlements and nearby hospitals which served the communities, located in four states in Peninsular Malaysia. The stool samples were examined for the presence of soil-transmitted helminth using real-time PCR and microscopy. The latter included the direct wet mount and formalin-ether concentration technique (FECT). The infection load in FECT-positive samples was determined by the Kato-Katz method. Rotorgene real-time analyzer detected five helminth species using two sets of assays. Results: The real-time PCR detected soil-transmitted helminth in 98.4% samples (n=122), which were 1.56 times higher than by microscopy. Ascaris lumbricoides and Trichuris trichiura were detected in more than 90% of the samples, while hookworm was detected in 46.7% (Necator americanus) and 13.9% (Ancylostoma sp.) of the samples. Comparison with previous reports on the Malaysian aborigines showed that the real-time PCR markedly improved the detection of Ascaris lumbricoides, hookworm and Strongyloides stercoralis. The real-time PCR detected poly-helminths in 92.6% of the samples compared to 28.7% by microscopy. In addition, 27 samples (22.1%) showed amplification of Strongyloides stercoralis DNA. Conclusions: The real-time PCR showed very high prevalence rates of soil-transmitted helminth infections in the aborigines and is the recommended method for epidemiological investigation of soil-transmitted helminth infections in this population.