There are several significant differences.
First, the steel on the Santoku knife is generally both harder and thinner. This makes for a much sharper edge, but also one more prone to chipping. A Santoku knife is less suitable for chopping than a chef's knife.
Second, the edge of a Santoku knife is usually straighter, with less curve or belly than a chef's knife. This means there will be less rocking motion possible with the knife, and so the user's technique must be different to accomplish similar tasks.
The Santoku is a fine kitchen knife, but is engineered different from a typical chef's knife. One can accomplish nearly all of the same tasks with the two knives, but with different techniques. The Santoku is -generally- harder to sharpen, more prone to chipping, and harder for Western-trained chef's to use. Once the user makes the necessary adaptations, the Santoku will hold a sharper edge longer.
I've studiously avoided saying that one is better than the other, as I don't believe this to be the case. They require different techniques, and have slightly different geometries.
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