As part of their preformulation evaluation, four in vitro protozoocidal 3,4-dimethyl-5-isoxazolylnaphthoquinones (ANQ-1-4) were investigated by differential scanning calorimetry (DSC), simultaneous differential thermal analysis-thermogravimetry-derivative thermogravimetry (DTA-TG-DTG), and Fourier transform infrared spectroscopy (FTIR). X-ray powder diffractometry (XRPD), thermomicroscopy and polarized light microscopy were used as an aid to interpret the thermoanalytical curves. The study demonstrated that the compounds are crystalline solids, unaffected by oxygen, safely manipulated at room temperature (RT) and also at higher temperatures as solids; however, all decompose exothermically at about their mp. Polycrystalline mixtures or undesirable solvates were not detected. All the compounds are insoluble in water and n-hexane and slightly soluble in ethanol, indicating that all are candidates to improve their solubilities in order to avoid formulation problems.