Recently, liquid chromatography-mass spectrometry (LC-MS) has been recognized as a useful method to analyze tetrodotoxin (TTX), the primary toxin for puffer fish poisoning. TTX usually exists with its chemically interchangeable analogs, such as 4-epiTTX and 4, 9-anhydroTTX. TTX and 4-epiTTX have the same molecular weight and the same fragmentation pattern by tandem mass spectrometry (MS-MS). In this study, we optimized conditions for hydrophilic interaction liquid chromatography (HILC)-MS-MS to quantitate TTX, 4-epiTTX, 4,9-anhydroTTX, and 5,6,11-trideoxyTTX with good separation. The relationships between the applied amounts of each TTX analog to the HILC-MS-MS instrument and the peak areas showed good linearity in the ranges examined. The lower limits of detection (signal-to-noise ratio = 3) were 64 pg on-column for TTX, 128 pg for both 4-epiTTX and 4,9-anhydroTTX, and 180 pg for 5,6,11-trideoxyTTX using an API 2000 mass spectrometer.