Access to an efficacious antimalarial drug is one of the cornerstones of the Roll Back Malaria initiative to decrease malaria morbidity and mortality. This is particularly important in emergency and post-emergency settings where access to treatment in the event of therapeutic failure may be restricted. In the aftermath of violence securing the independence of East Timor (1999), chloroquine continued to be used as first line therapy for the treatment of malaria. However, reliable data on the efficacy of chloroquine was not available. This paper represents the first attempt to document treatment failure with chloroquine in East Timor. The study was conducted using modified WHO guidelines in a rural hospital outpatient department in an area where there is seasonal transmission of both Plasmodium vivax and Plasmodium falciparum. 48 subjects presenting with fever and microscopically confirmed P. falciparum monoinfection were given supervised oral treatment with quality controlled chloroquine (25 mg/kg over 3 days) and followed clinically and parasitologically for 28 days. 32 of the 48 subjects had recurrent parasitaemia, and PCR confirmed that 28 of these were likely to be due to recrudescent parasites. The corrected treatment failure was, therefore, 58.3% (28/48), with all but one (2.1%) defined as late treatment failures (7-28 days after treatment). Further research into appropriate chemotherapy, including sulphadoxine-pyrimethamine and combination therapy for example with artemesinin or its derivatives, should be undertaken to select the most appropriate first line therapy for the management of uncomplicated malaria in East Timor.