The retention behavior of melamine (MEL), ammeline (AMN), ammelide, and cyanuric acid on various hydrophilic interaction liquid chromatography (HILIC) stationary phases was studied. Using fully optimized electrospray conditions and ammonium formate buffer pH 4/acetonitrile (20:80 v/v) as a mobile phase, precursor and product ions for each compound were identified. For the LC separation study, the effect of the following parameters was investigated: the type of buffer, the effect of the pH of ammonium formate buffer, the dilution percentage of the standard solutions in the vial, the stability of the standard solutions, and the column equilibration time. The retention and separation of melamine and its hydrolysis products on several HILIC columns was also investigated and retention models were proposed. Retention mechanisms were discussed for all the compounds. When the percentage of acetonitrile in the mobile phase was increased, the retention times of ammelide, ammeline and melamine were shifted to higher values, while the retention time of cyanuric acid did not change significantly. The separation of compounds with isobaric transitions (MEL, AMN) was achieved on four HILIC columns, namely TSKgel Amide-80, Luna HILIC, XBridge HILIC, and ZIC-HILIC (at either 10/90 or 15/85 ammonium formate buffer pH 4/ACN).