A simple and rapid method of analysis for the trace residue determination of enrofloxacin and its metabolite ciprofloxacin has been developed. Clean‐up of the samples is by cation exchange solid phase extraction (SPE) and determination made by high‐performance liquid chromatography using a base‐deactivated column and fluorescence detection. The method has been validated for the determination of residues in bovine and porcine muscle tissue and bacon. Recoveries at the 0.010 mgkg−1level for enrofloaxacin and ciprofloxacin respectively were 90%, 75% in bovine muscle, 75%, 54% in porcine muscle and 81%, 63% in bacon. Determination to the 0.001 mg kg−1level in bovine muscle and to the 0.002 mgkg−1level in porcine muscle and bacon was also carried out. The method has been used as a quantitative screening procedure.