In vitro drug susceptibility testing of Plasmodium falciparum must be conducted immediately after collecting a sample of the patient‘s blood; otherwise the parasites may weaken and the culture fail. Collecting blood samples from individuals in areas far from the field station or clinic where in vitro testing is conducted requires a reliable method of sample preservation during transportation. We examined and compared three different methods used to preserve blood samples in endemic areas in the Philippines. The three methods are as follows: the on-site method (test is conducted soon after blood sampling), flask culture method (sample is taken to the laboratory in a culture flask with medium) and EDTA tube method (sample is taken to the laboratory in a blood collection tube). The WHO in vitro micro-test for susceptibility of P. falciparum to chloroquine was performed using an AnaeroPack® system and a portable thermostat incubator. Evaluation of the three methods was based on schizont maturation, ease of handling, and risk of contamination during the test. The on-site and flask culture methods, but not the EDTA tube method, were effective for keeping the parasites viable. Furthermore, schizont maturation appeared better with the flask method than with the on-site method, especially in the control wells (drug-free wells). In addition, it was easier to perform the flask method than the on-site method. No contamination was observed using any of the methods. The results of the study suggest that the flask culture method is the most effective and useful way to preserve blood samples for the in vitro test and, moreover, that it aids in providing detailed field evidence of drug-resistant malaria.