The health impact of a Malaysian national helminth control program which provided school-based anthelmintic chemotherapy from 1974 to 1983 was re-visited after three decades post MDA and associated risk factors amongst urban poor communities identified. Stool samples collected were screened using the formalin ethyl-acetate concentration technique recovered at least one species of helminth and/or protozoan. Despite a steady decline observed between 1974-1983 however, post MDA infections continue to persist in pockets of communities moderately (18.9%; n=39/206) with higher infection recorded amongst PPR flat residents (22.5%, n=16/71). Among risk factors identified, waste management method was the primary factor for Ascaris lumbricoides infections (n=33; 16.0%), whereas age, education, employment and source of drinking water were significant risk factors for cryptosporidiosis. Despite the government’s efforts to improve health through the provision of basic amenities to the general public, higher prevalence values amongst PPR flat dwellers suggests the need to implement targeted chemotherapeutic treatment of, once a year deworming as recommended by World Health Organization when the baseline prevalence of soil-transmitted helminth infections in the community is over 20%, in addition to preventive measures though improvements in health awareness programs and improved waste management methods.