Northern Pakistan, Khyber Pakhtunkhwa (KP) is low malaria endemic area characterised by seasonal transmission with predominantly vivax malaria. Migration of high number of Afghan Refugees in 1978 into KP led to concerns for an increase in malaria, as the malaria incidence in this group was reportedly high compared to the local Pakistani population. Considerable progress has been made in controlling malaria through operational research in the camps where the Afghan refugees reside. However, this process requires effective, repeatable active surveillance tools for monitoring malaria control as availability of accurate data is the major challenge at present. The aim of this PhD project was to generate current information on malaria infection rates through parasite prevalence and malaria exposure using antimalarial antibody responses.The project also investigated the risk factors of malaria and heterogeneity in the geographic distribution of malaria in the camps by using GIS data with serological responses and parasite prevalence data. As an ancillary objective the project aimed to determine the prevalence of G6PO deficiency in the study population. A cross-sectional survey was conducted in five Afghan refugee camps of KP between June and September in 2010. Blood samples were obtained on filter paper from 2526 individuals and tested by rapid diagnostic test, paraSite species specific PCR and ElISA for antibody responses to Plasmodium vivax and Plasmodium falciparum. A questionnaire was administered to collect household and individual based information to determine the potential risk factors of malaria. Heterogeneity in malaria was observed between the studied camps based on seroprevalence, which ranged from 17%-45% for P. vivax and 3% to 11% for P. falciparum. Variation in P. vivax infection prevalence was also detected between the camps, which ranged from 0.4-9% (ROT) and 5-15% (peR). Variation in the distribution of malaria was also found within the camp using spatial/GIS data with clear foci of infection identified in 4 of 5 camps. The results showed that as expected parasite based prevalence measures (ROT and peR) are significantly lower than serological measure of exposure. P. falciparum infection prevalence (ROT and PCR) and seroprevalence was found to be extremely low with P. vivax infections predominant. Age seroprevalence changes were more pronounced for P. vivax than P. falciparum and seroconversion rate was strongly associated with parasite rate. Increasing age .and poorly built houses were associated with increasing risk, while staying in the same camp for the last 6 months and using measures to reducing vector biting such as repellents repellent, coils or insecticide spraying were associated with reduce risk of falciparum malaria. The risk of vivax malaria was observed to increase with increasing age, sharing house with cattle and having fever within 24 hours or two weeks and a reduction in the risk was seen in the individuals who reported use of Insecticide treated Bed Nets (ITN) night prior to surveyor used self protection measures from vector. The 563C-T polymorphism of G6PD gene was observed in only 2 unrelated individuals out of 505 individuals tested (O.4%). In conclusion, both parasitological and serological measures were able to detect spatial variation in infection and exposure to malaria at the micro epidemiological level within the camp. This data will help to provide beneficial and up-to-date information to manage control activities in the study area.