BACKGROUND: We have previously reported that rheumatoid arthritis patients, who adopted a modified Cretan Mediterranean diet, obtained a reduction in disease activity and an improvement in physical function and vitality. This shift in diet is likely to result in an altered intake of fatty acids. Therefore, the objective of the present study was to examine the dietary intake of fatty acids, as well as the fatty acid profile in serum phospholipids, during the dietary intervention study presented earlier. RESULTS: From baseline to the end of the study, changes in the reported consumption of various food groups were observed in the Mediterranean diet group. The change in diet resulted in a number of differences between the Mediterranean diet group and the control diet group regarding the fatty acid intake. For instance, a lower ratio of n-6 to n-3 fatty acids was observed in the Mediterranean diet group, both assessed by diet history interviews (dietary intake) and measured in serum phospholipids. Moreover, the patients in the Mediterranean diet group that showed a moderate or better clinical improvement during the study (diet responders), had a higher reported intake of n-3 fatty acids and a lower ratio of n-6 to n-3 fatty acids compared to the patients with minor or no improvement. Also the fatty acid profile in serum phospholipids differed in part between the diet responders and the diet non-responders. CONCLUSION: The changes in the fatty acid profile, indicated both by dietary assessments and through fatty acids in s-phospholipids may, at least in part, explain the beneficial effects of the Cretan Mediterranean diet that we have presented earlier.