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In order to overcome the problems associated with low water solubility, and consequently low bioavailability of active pharmaceutical ingredients (APIs), novel organic salts containing fluoroquinolones (e.g. ciprofloxacin and norfloxacin) were prepared, using an optimized synthetic procedure based on direct protonation, with different biocompatible counter ions such as mesylate, gluconate and glycolate. All the prepared organic salts were characterized by spectroscopic techniques, mass spectrometry and thermal analysis.Solubility studies in water and simulated biological fluids at 25 °C and 37 °C were also performed. Additionally, octanol-water and phospholipid-water partition coefficients were measured at 25 °C. The cytotoxicity and anti-inflammatory efficacy using an human cell model of intestinal epithelia (Caco-2 cells) were also evaluated and compared to those of the parent APIs. The adequate selection of the biocompatible anions allows the tuning of important physical, thermal and toxicological properties.