Estimates of phenoloxidase (PO) activity have been suggested as a useful indicator of immunocompetence in arthropods, with the idea that high PO activity would indicate high immunocompetence against parasites and pathogens. Here, we test for variation in PO activity among clones of the planktonic crustacean Daphnia magna and its covariation with susceptibility to infections from four different microparasite species (one bacterium and three microsporidia). Strong clonal variation in PO activity was found within and among populations of D. magna, with 45.6% of the total variation being explained by the clone effect. Quantitative measures of parasite success in infection correlated negatively with PO activity when tested across four host populations. However, these correlations disappeared when the data were corrected for population effects. We conclude that PO activity is not a useful measure of resistance to parasites or of immunocompetence within populations of D. magna. We further tested whether D. magna females that are wounded to induce PO activity are more resistant to infections with the bacterium Pasteuria ramosa than non-wounded controls. We found neither a difference in susceptibility nor a difference in disease progression between the induced group and the control group. These results do not question the function of the PO system in arthropod immune response, but rather suggest that immunocompetence cannot be assessed by considering PO activity alone. Immune response is likely to be a multifactorial trait with various host and parasite characteristics playing important roles in its expression.