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Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR) has the potential to become a new diagnostic tool for malaria and other diseases. For point-of-care testing, the use of ATR-FTIR in malaria diagnosis enables the analysis of blood in the aqueous state, which represents an enormous advantage by minimising the sample preparation by removing the need for cell fixation. Here we report the quantification of malaria parasitemia in human RBCs in their normal physiological aqueous state. A potential confounding variable for spectroscopic measurements performed on blood are the various anticoagulants that are required to prevent clotting. Accordingly, we tested the effects of 3 common anticoagulants; Sodium Citrate (SC), Potassium Ethylenediaminetetraacetic Acid (EDTA) and lithium heparin on plasma and whole blood in the aqueous and dry phase. Principal Component Analysis (PCA) revealed the model was heavily influenced by the anticoagulants in the case of dry samples, however, in aqueous whole blood samples, the effect was less pronounced as the water in the sample presumably diluted the amount of anticoagulant in contact with the ATR crystal. The possible influence of the anticoagulant effect on the ability to quantify parasitemia levels was tested using Partial Least Squares Regression Analysis (PLS-R). There was no influence of anticoagulants on quantification in the 0–1% range, however attempts to quantify at lower levels (0–0.1%) was best achieved with heparin compared to the other two anticoagulants. The results demonstrate ability to diagnose malaria using ATR-FTIR spectroscopy using wet RBC samples as well as underscoring the desirability to perform wet measurements as these minimise the possible confounding influence of anticoagulants used in blood collection.