Cost-effectiveness information on where malaria rapid diagnostic tests (RDTs) should be introduced is limited. We developed incremental cost-effectiveness analyses with data from rural health facilities in Ghana with and without microscopy. In the latter, where diagnosis had been presumptive, the introduction of RDTs increased the proportion of patients who were correctly treated in relation to treatment with antimalarials, from 42% to 65% at an incremental societal cost of Ghana cedis (GHS)12.2 (US$8.3) per additional correctly treated patients. In the "microscopy setting" there was no advantage to replacing microscopy by RDT as the cost and proportion of correctly treated patients were similar. Results were sensitive to a decrease in the cost of RDTs, which cost GHS1.72 (US$1.17) per test at the time of the study and to improvements in adherence to negative tests that was just above 50% for both RDTs and microscopy.