The objective of present study was to prepare positively charged ciprofloxacin-loaded nanoparticles providing a controlled release formulation. The particles were prepared by water-in-oil-in-water (w/o/w) emulsification and solvent evaporation, followed by high-pressure homogenisation. Two non-biodegradable positively charged polymers, Eudragit® RS100 and RL100, and the biodegradable polymer poly(lactic-co-glycolic acid) or PLGA were used alone or in combination, with varying ratios. The formulations were evaluated in terms of particle size and zeta potential. Differential scanning calorimetry measurements were carried out on the nanoparticles and on the pure polymers Eudragit® and PLGA. Drug loading and release properties of the nanoparticles were examined. The antimicrobial activity against Pseudomonas aeruginosa and Staphylococcus aureus was determined. During solvent evaporation, the size and zeta potential of the nanoparticles did not change significantly. The mean diameter was dependent on the presence of Eudragit® and on the viscosity of the organic phase. The zeta potential of all Eudragit® containing nanoparticles was positive in ultrapure water (around +21/+25 mV). No burst effect but a prolonged drug release was observed from all formulations. The particles’ activity against P. aeruginosa and S. aureus was comparable with an equally concentrated ciprofloxacin solution.