Japanese people consume significant amounts of long chain n-3 polyunsaturated fatty acids (PUFAs) derived from fish, but the association of PUFAs with cancer mortality has not been fully investigated. To study geographic differences in n-3 PUFAs intake, we compared serum fatty acid and dietary fish intake among various Japanese populations having different rates of cancer mortality. The subjects were 50 men from each of five regions in Japan and 47 Japanese men from Sao Paulo, Brazil. All were randomly selected and aged 40 to 49 years. Serum fatty acids were measured by gas chromatography and the frequency of fish intake was obtained by a food frequency questionnaire. Significant geographic differences in serum fatty acid levels (% of total fatty acids) and fish intake (days/4 weeks) were observed. The percentages of serum total PUFA were similar in the six regions, though there was an almost three-fold difference in n-3 PUFAs content between Brazil (3.9%) and Akita (10.9%). The frequency of total fish intake corresponded to serum n-3 PUFAs composition. The relationship between cancer mortality and serum n-3 PUFAs levels was not clear, though an inverse association between prostate cancer and serum n-3 PUFAs levels appeared to exist. The results suggest that although serum n-3 PUFAs varied significantly, the observed geographic difference did not account for the different cancer risks at the population level.