We evaluated the proportion of variants of circumsporozoite protein (cp) gene 26 and cp29 antigenic epitopes of Plasmodium falciparum infecting patients among 3 provinces in western Thailand, in addition to published variants from Gambia. The proportion of patients coinfected with cp26 and cp29 strains was significantly higher in patients reporting to malaria clinics in Tak than in Kanchanaburi and Ratchaburi and higher in Kanchanaburi than in Ratchaburi. In western Thailand, coinfection with cp26 and cp29 appears to increase with increasing latitude. There were also significant differences in proportion of these variants among Thai provinces and Gambia. An association of patient human leukocyte antigen (HLA) class II genotype was associated with P. falciparum strains. There were significant associations among the HLA-DQA alleles in patients, the province of origin, and cp variants of P. falciparum.