Japanese 'Fuji' apples are exported almost exclusively to the Taiwanese market, where they compete mainly with apples from South Korea and the USA. The objective of this study was to determine the geographical origin of 'Fuji' apples on the basis of their elemental composition. Concentrations of 10 elements (B, Mn, Fe, Cu, Zn, Sr, Ba, Ni, Ti, Al) were determined by inductively coupled plasma atomic emission spectroscopy (ICP-AES) from the peduncles and seeds of 63 domestic samples originating from Japan and 40 foreign samples from the USA, South Korea and China. Because concentrations of these elements in the apple peduncles and seeds were higher than those in the rinds or sarcocarps, we determined that peduncles and seeds were more suitable parts for measuring the elemental concentrations to distinguish the geographical origins. By using the linear discriminant analysis results for 7 elements (B, Mn, Fe, Cu, Zn, Sr, Ba) measured either in the peduncles or in the seeds, we classified the origin of the apples (domestic or foreign) with 96.1% accuracy. By using canonical discriminant analysis results for all 10 elements of the peduncles and 8 elements of the seeds, we classified the origins of foreign apples (China, South Korea or the USA) with 97.5% accuracy. By using canonical discriminant analysis of the results for 7 elements of both the peduncles and the seeds, we classified the origins of apples found in the Taiwanese market (Japan, South-Korea, or the USA) with 98.9% accuracy. Based on these results, we attained a reliable determination method of the Japanese geographical origin of 'Fuji' apples.