Apple juice samples intended for infants purchased in Navarra (Spain) have been analyzed for PAT occurrence. Two capillary electrophoresis methods, based on a MEKC and a CEC system, and an HPLC method were evaluated for the aforementioned study. The CEC system gave less satisfying separations and several practical problems, so samples have been analyzed by MEKC and HPLC. Both methods have been comparable in terms of recovery, precision, limits of detection, volume of organic solvents used and adequate selectivity with regard to PAT and HMF. The analysis time in HPLC has been slightly lower than in the MEKC methodology. The PAT levels obtained in apple juice by both validated methods showed a strong correlation (p<0.001). Therefore, both methodologies are useful for the accurate quantification of patulin in this matrix. The PAT levels obtained in the 20 infant apple juices samples were in a range between