The application of PCR for the diagnosis and the characterisation of parasites is discussed using four examples. (1) A PCR assay that was developed for the detection of Leishmania was shown to be as highly sensitive as in vitro cultivation of the parasites from lymph node aspirates and bone marrow biopsies. (2) Single eggs of Echinococcus multilocularis can principally be detected and identified by PCR. However, a cumbersome sample preparation is inevitable in order to remove PCR-inhibitory substances present in fox faeces. (3) Analysis of the amplified SSU rRNA gene of Encephalitozoon-like isolates from humans, rabbits and farm foxes confirmed for the first time that E. cuniculi-isolates from humans and animals are indistinguishable and that they are of importance as opportunistic parasites in HIV-infected patients. (4) Swiss isolates of Giardia originating from humans, calves, sheep and a dog could be allocated into three distinct genetic groups by analysing several PCR-amplified genes that encode for variant-specific surface proteins. There was no evidence for the presence of host-specific genotypes.