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Abu Sa'id al-Khudri reported that a person came to Allah's Messenger (may the peace and blessings of Allah be upon him) and told him that his brother's bowels were loose. Thereupon Allah's Messenger (may the peace and blessings of Allah be upon him) said:
Give him honey. So he gave him that and then came and said: I gave him honey but it has only made his bowels more loose. He said this three times; and then he came the fourth time, and he (the Holy Prophet) said: Give him honey. He said: I did give him, but it has only made his bowels more loose, whereupon Allah's Messenger (may the peace and blessings of Allah be upon him) said: Allah has spoken the truth and your brother's bowels are in the wrong. So he made him drink (honey) and he was recovered.
The Prophet (may the peace and blessings of Allah be upon him) was famous among his companions for medicine and wisdom. He knew how to diagnose the disease and prescribe the medicine, this is one of his insights, with which Allah has singled out him. He was accessible to anyone who likes to ask about the religious rulings or even the one who has personal needs of his own or one of his brothers. The Prophet (may the peace and blessings of Allah be upon him) would provide a convincing answer, he may be inspired directly from Allah or that he would receive the revelation from Gabriel - peace be upon him - and do what he recommends.
I have read in some books that if the one suffering from intestinal pain drank honey he would experience diarrhea, then the bacteria that cause the disease will gradually go out and he will be healed by the permission of Allah.
The honey has some healing, at some time, for a disease, and for someone, it is not a cure of all the diseases instantly, or for all people as some people assume.
What is proven and supported by the reality is that it is a cure for many incurable diseases, but not for all the diseases, nor for all the persons. But It is as we said a healing of some diseases… to the last thing we mentioned.
In this commandment, the certainty of the Prophet (may the peace and blessings of Allah be upon him) shows that honey is the successful treatment of abdominal diseases in general.
This does not prevent the presence of medicines other than honey, nor does it prevent the presence of diseases other than those which were prevalent in his time, honey does not benefit as a treatment for them. Since there is no text in the Qur'an or in the Prophetic Sunnah that indicates the generalization.