Molecular diagnostics have the potential to detect parasites at lower intensities than direct inspection such as microscopy. However, techniques using the polymerase chain reaction (PCR) are sufficiently complex that different laboratories may implement them with varying attention to purity of DNA, recognition of artifacts, and resolution of multiple bands. The result is that some laboratories may be unable to get a published protocol to work or abandon it prematurely. Comparisons of prevalance of maleria in the blood of birds involving the same primers with different implementations show that the original published implementation was most accurate. In particular, false negatives by PCR in samples where parasites can be detected by microscopy reflect problems with laboratory procedure.