I know that it tends to stretch the front ligaments of the knee and might lead to knee problems later in life. I know a shihan (7th Dan) who you will never see sitting in seiza unless he's doing suwari waza.
In my mind, the whole notion of sitting in seiza for long periods of time seems a bit extreme. I don't understand the point of it. Perhaps Peter or someone else in Japan can give us a Japanese perspective on it.
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