A robust method was developed and validated for analyzing tetrodotoxin and its analogues (TTXs) in high- and low-fat tissues of pufferfish using LC–MS/MS. The tissue distribution of TTXs in four Takifugu pufferfish species and their phenotypic variants was determined using the validated method. A significant matrix effect was shown, and the matrix-matched TTX calibration curves (r2 > 0.999) were used for the analysis of TTX. The method detection limit for TTX ranged from 0.006 to 0.009 μg/g. Recoveries from TTX-fortified tissue samples (0.1–2.0 µg/g) were in the range of 96.1–107.3 % with RSDs less than 7.8 %. TTX levels in the pufferfish tissues reached a maximum of 1.32 × 104 µg/g. The developed method was used for the relative quantification of TTX analogues. The major TTX analogues were deoxyTTXs (i.e., trideoxy-, dideoxy-, and deoxyTTX). The ovary and liver of pufferfish showed higher concentrations of TTXs compared to other tissues. The developed method was successfully validated and applied to Korean pufferfish samples.