This study describes lipid composition and antioxidants of Baltic cod Gadus morhua L. during the reproductive cycle, and investigates whether they reflect its dominant prey and whether levels of fatty acids important for reproductive performance were low. Reasons for a shift in peak spawning time of Baltic cod from spring/early summer to midsummer since the early 1990s remain unresolved and may partly be diet related. This study demonstrated that a substantial amount of lipid was invested in cod ovarian development, and that lipid composition varied substantially with the reproductive cycle. Selective retention of the essential fatty acids docosahexaenoic acid (DHA) and arachidonic acid (ARA) in ovaries during maturation was evident, but despite mobilization from the liver, ARA levels were low in ovaries during late maturation and spawning. Astaxanthin and a-tocopherol accumulated in cod ovaries and decreased in late maturing and spawning fish, most likely due to their antioxidant protection activity. The fatty acid composition of cod liver reflected its clupeid prey. The ratio of 18:1n-9 to DHA was almost twice as high in sprat as in herring and indicated the ratio of sprat and herring in cod diet, while the level of 16:1n-7 and astaxanthin indicated the presence of the isopod Saduria entomon in cod diet. It is likely that food web alterations in the Baltic ecosystem related to environmental and hydrographic changes caused a decrease in ARA availability. Low ARA content coincides with cod ovarian development in the central Baltic Sea, and may be associated with the delay in spawning and affect egg and larval survival; however, this needs further verification in experimental studies.