In this study, a hydrophilic interaction liquid chromatography–mass spectrometry (HILIC-MS/MS) method for the determination of benzalkonium (BAC) homologues and didecyldimethylammonium (DDAC) was developed. A satisfactory chromatographic separation of BAC homologues and DDAC was achieved using, as mobile phase, acetonitrile–aqueous 50 mM ammonium formate (pH 3.2) (93 + 7 v/v) at 0.3 mL min−1. The elution order of BAC homologues was from benzyldimethylhexadecylammonium chloride (C16-BAC) to benzyldimethyldecylammonium chloride (C10-BAC), the exact opposite with respect to separation using reversed liquid chromatography. The instrumental method was successfully applied to powdered and liquid milk for infants (about 50 samples). From powdered milk samples, BAC and DDAC were extracted using 5 % formic acid in methanol for 60 min at 60 °C in an ultrasonic bath; after dilution with water and 5 % NH4OH solution, a purification step using a weak cationic exchange column was performed. Satisfactory limit of detections (LODs) were achieved, below 1.0 μg kg−1 and 0.05 μg L−1 for powdered and liquid milk for infants, respectively. No sample was free of BAC homologues and DDAC, and in one powdered milk sample, the contamination level exceeded 500 μg kg−1, the maximum level recommended by the Standing Committee on the Food Chain and Animal Health for food and feed.