Objective To investigate the failure of treatment with chloroquine in Yunnan in order to help formulate adequate antimalarial drug policy. Methods A World Health Organization 28-day in vivo test on therapeutic response for uncomplicated falciparum malaria in area with low or moderate transmission was adopted. Patients of age ≥ 6 months old were admitted without limitation in density of parasitaemia and body temperature. Clinical and parasitological observation was conducted for patients on day 0, 1, 2, 3, 4, 7, 14, 21, 28 and 35. Results Of 62 patients identified as malaria cases infected by Plasmodium falciparum only, Plasmodium vivax only or by both species, 52 cases infected by Plasmodium falciparum only were included in the study. The overall treatment failure rate was 40.7%, with early treatment failure (ETF) rate of 1.8% and late treatment failure rate (LTF) of 38.9%. Conclusion The treatment failure rate was much higher than the rate of 25% recommended by WHO. It is suggested that use of single chloroquine should be stopped in the treatment of falciparum malaria cases in such area. No relationship was found between the failure rate and the density of malaria parasites.