Docosahexaenoic acid (22:6n-3, DHA) is highly enriched in membrane of brain and retina, and plays an important role in maintaining an optimal function of the central nervous system. We investigated the effect of n-3 fatty acid deficiency on rat brain, retina and liver fatty acyl composition at two different ages (3 wks and 15 wks) under DHA deficient condition. Rat pups born to dams fed a diet with $3.1\%$ of total fatty acids as $alpha-linolenic$ acid (LNA) were fed using an artificial rearing system either an n-3 deficient (n-3 Def) or n-3 adequate (n-3 Adq) diet. Both diets contained $17.1\%$ linoleic acid (LA) but the n-3 Adq diet also contained $3.1\%$ LNA. Rats consuming the n-3 Def diet showed a lower brain $(50\%;in;13;wks;and;70\%;in;15;wks,;p<0.05)$ and retinal $(50\%;in;13;wks;and;63\%;in;15;wks,;p<0.05)$ DHA than those on the n-3 Adq diet, which was largely compensated for by an increase in docosapentaenoic acid (22:5n-6, DPAn-6). In the liver of the n-3 Def group, the percentage of DHA decreased by $97\%$ at 3 wks of age with an apparent increase in DPAn-6 relative to the n-3 Adq group (p<0.05), while there was a $65\%$ lower liver DHA in n-3 Def group at 15 wks of age than the n-3 Adq group (p<0.05). Liver arachidonic acid (20:4n-6, AA) was increased at 3 wks of age but decreased at 15 wks of age in the n-3 Def group compared with n-3 Adq group (p<0.05). In conclusion, the replacement of DHA by DPAn-6 in brain and retina fatty acid composition may be related to the suboptimal function in spatial learning, memory and visual acuity. This artificial rearing method presents a first generation model for n-3 deficiency that is similar to the case of human nutrition that commonly employed two generation model.