It is commonly assumed that the most accurate data on fatty acid (FA) contents are obtained when samples are analyzed immediately after collection. For logistical reasons, however, this is not always feasible and samples are often kept on ice or frozen at various temperatures and for diverse time periods. We quantified temporal changes of selected FA (μg FAME per mg tissue dry weight) from 6 fish species subjected to 2 handling and 3 storage methods and compared them to FA contents from muscle tissue samples that were processed immediately. The following species were investigated: Common Carp (Cyprinus carpio), Freshwater Drum (Aplodinotus grunniens), Channel Catfish (Ictalurus punctatus), Antarctic Eelpout (Pachycara brachycephalum), Rainbow Trout (Oncorhynchus mykiss) and Arctic Charr (Salvelinus alpinus). The impact of storage method and duration of storage on FA contents were species-specific, but not FA-specific. There was no advantage in using nitrogen gas for tissue samples held on ice for 1 week; however, holding tissue samples on ice for 1 week resulted in a loss of FA in Charr. In addition, most FA in Trout and Charr decreased in quantity after being stored between 3 and 6 hours on ice. Freezer storage temperature (-80 or -20°C) also had a significant effect on FA contents in some species. Generally, we recommend that species with high total lipid content (e.g. Charr and Trout) should be treated with extra caution to avoid changes in FA contents, with time on ice and time spent in a freezer emerging as significant factors that changed FA contents.