Antioxidant defence plays a crucial role in rapidly growing and multiplying organisms, including parasites and tumor cells. Apart from reactive oxygen species (ROS) produced in endogenous reactions, parasites are usually exposed to high ROS concentrations imposed by the host immune system. The glutathione and thioredoxin systems represent the two major antioxidant defence lines in most eukaryotes and prokaryotes. Trypanosomatids, however, are characterized by their unique trypanothione system. These systems are NADPH-dependent and based on the catalytic activity of the flavoenzymes glutathione reductase, trypanothione reductase and thioredoxin reductase (TrxR), respectively. TrxR reduces the 12-kDa protein thioredoxin (Trx), which in turn provides elcctrons to ribonucleotide reductase, thioredoxin peroxidases (TPxs), certain transcription factors and other target molecules. Comparing the thioredoxin systems of different parasites and their respective host cells enhances our understanding of parasite biology and evolution, of parasite-host interactions and mechanisms of drug resistance. It furthermore opens avenues for the development of novel antiparasitic compounds. Here we review the current knowledge on the Trx systems of eukaryotic parasites, finally focusing on the malarial parasite Plasmodium falciparum.