Consumption of fish oil and dietary supplements containing eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) has steadily increased because of their reported health benefits. A rapid procedure based on Fourier Transform Near Infrared Spectroscopy (FT-NIR) models was developed for analysis of fish oil and their ethyl ester derivatives to replace the time consuming GC method. Inclusion of fish oil or ethyl esters containing varied concentrations of OA, EPA, and DHA into the FT-NIR classification models made possible their classification and quantification. Accurate GC analysis is essential in developing reliable quantitative models since FT-NIR is matrix dependent. Development of FT-NIR models based on 30 m PEG capillary GC column results, as recommended by the official GC method for analysis of marine oils, proved problematic, since these columns did not resolve many geometric isomers compared to 100 m highly polar cyanopropyl polysiloxane columns. Depending on the content of geometric isomers in fish oils and ethyl esters, the levels of long-chain n-3 PUFA would be overestimated if the model used were based on the results from a 30 m column. The FT-NIR method was found to be applicable to all fish oil and ethyl ester samples, except when fatty acids were outside the range examined, or contaminants were present. The FT-NIR method was applicable to analysis of in-plant intermediates provided contaminants were absent, or identified so they could be incorporated into the model. The FT-NIR method was suitable to evaluate the shelf life of n-3 PUFA concentrates.