Several studies on lipid stability of freeze-dried fish pointed out the relationship between relative humidity (RH) and autoxidation of highly unsaturated fatty acids. The present study shows the changes of tissue lipids in two different fish, freeze-dried and stored under various RH conditions. Fillets of Scomber scomber L and Sardina pilchardus sardina were freeze-dried and stored for 1, 3, 6 and 9 months. periodically, the sample of both fish were analyzed to evaluate the autoxidation of lipids. The results show that the autoxidation of lipids is quicker during 1st-3rd month of storage, while in a high humidity environment the tissue lipids change slower. According to these results both time of storage and relative humidity must be controlled to maintain the nutritive value of freeze-dried fish.