The protozoan parasite Leishmania is a folic acid auxotroph. Previous work has led to the characterization of the main folate transporter FT1. FT1 is part of the folate/biopterin transporter (FBT) family and Leishmania with its 14 members is, of all sequenced organisms, the one with the most FBTs. We developed a real-time TaqMan RT-PCR assay to follow the expression of these FBT genes during growth phases, life cycles and in methotrexate-resistant mutants of Leishmania infantum. FT1 is expressed preferentially in the logarithmic phase which is consistent with the higher accumulation of folate in that stage. FT1 RNA levels even seemed to be related to folate concentration in the medium. Surprisingly, several of the FBT genes were expressed preferentially in the stationary phase of growth, a stage with minimal folate accumulation. It suggests that these FBT members may transport other related substrates. Resistance to methotrexate is associated with FT1 inactivation and upregulation of other FBT genes. Inactivation of FT1 is due either to a gene deletion mediated by homologous recombination between conserved FBT sequences or by segmental gene conversion. This study highlighted the multiplicity of FBT genes in Leishmania, their complex RNA expression, and novel gene rearrangements associated with FT1 inactivation and antifolate resistance.