Development of methods for the manipulation of the genomes of parasitic protozoa will lead to enhanced understanding of parasite biology and host-parasite relationships. Efficient gene transfer and targeted integration by homologous recombination were achieved in the parasitic protozoan Trypanosoma brucei, the causative agent of sleeping sickness. An expression vector with the neomycin phosphotransferase gene (neo), under the control of a procyclic acidic repetitive protein (PARP) gene promoter, was targeted into an intergenic region in βα-tubulin-gene tandem array. Sixteen copies of neo were found in a tandem array in one of the transfectants where the PARP promoter controlled α-amanitin-resistant transcription of neo, whereas transcription of tubulin genes remained α-amanitin-sensitive.