We tested whether contamination of avian blood by the parasite Haemoproteus could cause the amplification of false positive genetic markers generated by random amplified polymorphic DNA (RAPD). DNA was extracted from blood taken from five Rock Doves (Columba livia) infected with Haemoproteus, and one uninfected control individual. A drug treatment was administered to clear the infection, and a second DNA sample extracted. The parasitized and unparasitized DNA samples were used in RAPD reactions with 20 different 10-nucleotide primers, which produced 178 well-resolved markers. In no case were any of the reaction products specific to the parasitized samples, and in almost all cases the products were found consistently across all replications of infected and non-infected samples. The high ratio of avian to parasite DNA and the greater genome complexity of the host probably prevents the amplification of markers unique to parasite species such as Haemoproteus.