A method for the analysis of enrofloxacin and ciprofloxacin in chicken muscle using marbofloxacin as internal standard is proposed. Clean-up and pre-concentration of the samples are effected by solid-phase extraction and determination is carried out by capillary electrophoresis using a photodiode array detector. The calibration graphs are linear for enrofloxacin and ciprofloxacin from 10 to 300 μg/kg. The method recoveries for enrofloxacin and ciprofloxacin are 74 and 54%, respectively. The limit of detection for the two compounds is lower than 25 μg/kg, which allows the detection of positive muscle samples at the required maximum residue limits.