Because of the widespread presence of chloroquine-resistant Plasmodium falciparum malaria, mefloquine is now the recommended drug of choice for long-term malaria prophylaxis in these areas. Although several studies have compared plasma and whole blood concentrations of either mefloquine or its carboxylic acid metabolite, we report the first comparison of serum and whole blood levels in 86 Dutch marines taking 250 mg of mefloquine weekly for 18 weeks while deployed in western Cambodia. All samples were taken during steady-state and at 42–48 hr after the most recent dose. The concentration of mefloquine in serum (mean = 979 ng/ml) was significantly greater than in whole blood (mean = 788 ng/ml) (P < 0.00001, by paired t-test) with an overall mean ratio of 1.28. The concentration of the metabolite in serum (mean = 3,039 ng/ml) was also significantly greater than in whole blood (mean = 1,390 ng/ml) (P < 0.00001, by paired t-test) with an overall mean ratio of 2.25. These findings are similar to previous reports of plasma-to-whole blood levels. Furthermore, we report that the within-individual ratios of the metabolite concentration to the mefloquine concentration were also found to be significantly different in serum (3.79; P < 0.00001, by paired t-test) and in whole blood (2.02; P < 0.00001, by paired t-test). Appropriate attention must be given to these differences when comparing serum and whole blood concentrations of either mefloquine or its metabolite to avoid misinterpretation of their respective levels. Also, the determination of the relative mefloquine ratios in various blood fluids, as well as the documentation of the metabolite levels and their ratios, is critical to the appropriate interpretation of both chemoprophylaxis and chemotherapy, especially in the presence of resistant strains.