The isothiocyanate (ITC) yield of wasabi, the Japanese horseradish (Wasabi japonica), was measured on its release from glucosinolates in the rhizomes of plants grown in two traditional ways. Mature plants of 18 months old were harvested from two different commercial farms located in the South Island of New Zealand. At one farm, the plants were grown in raised soil beds, while the plants at the other farm were grown in gravel irrigated by river water. Following harvest, the rhizomes from each growth medium were divided into five size groups based on the weight and length of the rhizomes. The different sized rhizomes were also subdivided into proximal, medial, and distal portions of the rhizomes and each portion was further subdivided into epidermis plus cortex, and vascular plus pith. The individual and total ITC contents of each portion (proximal, medial, and distal) of the rhizomes were measured using dichloromethane extraction followed by the GC-FPD. The total ITC content of the rhizomes grown in soil increased (13 times) linearly from 6 to 114 g of rhizome weight, while the mean ITC content of the water-grown wasabi increased (10 times) nonlinearly for similar sized rhizomes. Water-grown rhizomes in the weight range from 18 to 45 g gave significantly (P = 0.030) higher total ITC (1-2 times) than similarly sized soil-grown rhizomes. Analysis of the tissues showed that the total and the individual ITCs were found in significantly higher levels (73 and 64%, respectively) in the skin and cortex tissue compared to the vascular and pith tissues. Analysis of the ITC content of the different locations of the wasabi rhizome showed that the distal portion of the rhizome contained significantly higher levels of both total and individual ITCs compared to the medial and proximal portions of the rhizome.