The WHO recommends artemisinin as the first-line treatment against malaria and it currently treats around 280 million cases of malaria every year. Resistance to artemisinin derivatives was initially reported in western Cambodia and has now spread to Thailand, Vietnam and Myanmar. The spread of artemisinin resistance will have profound consequences for morbidity and mortality associated with malaria globally, as there are currently no new antimalarials available that could replace artemisinin. As the genetic mechanism for artemisinin resistance is unknown, resistance is detected by examining parasite clearance curves in therapeutic efficacy trials. However, naturally acquired immunity to malaria will also influence parasite clearance curves. In malaria endemic areas, immunity to malaria can develop after repeated exposure and can reduce clinical symptoms and high-density parasitaemia in the blood. We hypothesise that naturally acquired host immunity may impede the assessment of parasite clearance rates after drug treatment because it increases the probability of parasite clearance independently of antimalarial drugs. The objective of our study was to examine the interaction between host immunity and parasite clearance on the Thai-Myanmar border. A recent longitudinal study at the Thai-Myanmar border showed that slow-clearing infections after artemisinin treatment have increased from 0.6% in 2001 to 20% in 2010. We determined antibody levels to MSP1-42, AMA1 and EBA140 in 1146 dried blood spot samples from this longitudinal study (2007-2011) and related levels to parasite clearance rates. We found that immunity influenced parasite clearance rates after artemisinin treatment, with individuals having higher levels of immunity having faster parasite clearance times. Immunity is therefore an important confounder in the assessment of emerging artemisinin resistance and will impact on worldwide resistance monitoring and surveillance efforts.