Malaria is still endemic in Sarawak and Sabah. Numerous studies have indicated that patients with malaria are commonly co-infected with helminthes particularly in endemic regions. The aim of this study was to investigate the incidence of soil-transmitted helminth (STH) infection among malaria patients using microscopy and multiplex real-time PCR at two district hospitals in Sarawak. A total of 94 patients who were clinically-suspected to have malaria were confirmed to be infected by both microscopy and multiplex real-time PCR. By the molecular method, 23.4%, 74.5% and 2.1% of the samples were positive for Plasmodium falciparum, P. vivax and mixed P. falciparum and P. vivax, respectively. Among the malaria patients, 48.9% were found to be co-infected with STHs. In comparison, microscopic examinations showed that 6.4% of the malaria patients were infected with STHs. From the real-time PCR positive samples, 31.9% had single helminth infections while 17% had mixed infections. In conclusion, this study showed that almost half of the malaria patients at the two Sarawak hospitals were co-infected with helminth. Future studies should be specifically designed to determine if there is any correlation between the two infections in terms of incidence and intensity.