Plasmodium falciparum undergoes antigenic variation by switching the expressed erythrocyte membrane protein (PfEMP)1. This family of proteins plays an important role in the development of chronic, recrudescent P. falciparum malaria, acquired immunity and severe malaria. However, little is known about the switching mechanism or switching rates in the human host. Here, we estimate the switch rate of var genes, using recently published data describing the var gene transcripts detected in blood taken from human volunteers during acute P. falciparum infections and a mathematical model of the in-host dynamics. The overall switch rate of PfEMP1 predicted during the initial stage of infection ( approximately 18% switching parasites per generation) is much higher than previously reported. The implications of the predicted switching rates are discussed.