Near infrared spectroscopy (NIR) was applied to estimate lipid composition and degradation of two lean fish species, saithe (Pollachius virens) and hoki (Macruronus novaezelandiae). Calibration models were developed, using partial least squares (PLS) regression, for total lipid content and composition, free fatty acids (FFA), thiobarbituric acid reactive substances (TBARS) and fluorescent interaction compounds (OFR). Coefficients of determination for calibration (R2cv) and root-mean-square error of cross validation (RMSECV) ranged from 0.82 to 0.99 and 0.66 to 3.69 for hoki and from 0.64 to 0.99 and 0.06 to 2.65 for saithe, respectively. The validations of the calibrations indicated that lipid composition and FFA of hoki and saithe can be estimated by NIR with good accuracy. Furthermore, NIR differentiates fish muscles with low, medium and high concentration of OFR and TBARS. Overall, the results demonstrate the potential for use of NIR spectroscopy as an objective and non-destructive method to inspect the lipid characteristics and quality of frozen lean fish.