A new chiral analytical method based on CF-MS is proposed for the identification and simultaneous quantification Of D/L-carnitine in infant formulas. Previous derivatization of carnitine with FMOC enabled the optimization of the chiral separation using CE with UV detection. An optimization of electrospray-MS parameters using a partial filling of the non-volatile chiral selector (succinyl-gamma-CD) was performed. A selective fragmentation using MS2 experiments with an ion trap analyser was carried out to confirm the identity of D/L-carnitine according to the current legislation. Satisfactory results were obtained in terms of linearity, precision, and accuracy. Interestingly, the CE-MS2 method developed allowed a sensitivity enhancement with respect to UV detection of 100-fold, obtaining an LOD of 100 ng/g for D-carnitine. The determination of L-carnitine and its enantiomeric purity in 14 infant formulas supplemented with carnitine was successfully achieved, sample preparation only requiring an ultrafiltration with centrifugal filter devices to retain the components with the highest molecular weights.