Present study includes the comparison of methods of external and internal standard for the estimation of parameters like linearity and precision in gas chromatographic analysis of docosahexaenoic acid (DHA) with flame ionization detector at temperature 140°C -280°C and using hydrogen as gas carrier. Linear dependence of the ratio of area of methylated DHA/area of methyl nonadecanoate (internal standard) to the DHA concentration was obtained. There was no observed difference between the correlation coefficients for two methods (R 2 = 0.9928). From the experimental results, it is obvious that related standard deviation (RSD) for internal standard method is more than RSD for external standard method, which demonstrates that nonadecanoic acid is not a suitable internal standard. The external standard method allows achievement of good linearity and precision and is appropriate for identification and determination of DHA and fatty acids in food supplements.