A capillary gas chromatography method using a flame ionization detector has been developed for the trace analysis of allylamine (AA) in sevelamer hydrochloride (SVH) and sevelamer carbonate (SVC) drug substances. The method utilized a mega bore capillary column DB-CAM (30 m × 0.53 mm × 1.0 μm) with a bonded and cross-linked, base-deactivated polyethylene glycol stationary phase and was validated for specificity, sensitivity, precision, linearity, and accuracy. The detection and quantitation limits obtained for allylamine were 2 μg/g and 6 μg/g, respectively. The method was found to be linear in the range between 6 μg/g and 148 μg/g with a correlation coefficient of 0.9990. The average recoveries obtained in SVH and SVC were 93.9% and 99.1%, respectively. The developed method was found to be robust for the determination of AA in sevelamer drug substances and also the specificity was demonstrated with a gas chromatograph coupled with a mass spectrometer.