From "Regulations of Worship During Menses" by Muhammad al-Jibaly Available from:

 “Chapter 6:  Entering the Masjid

  Some of those who prohibit a person in janabah or menses from entering the masjids cite the following ayah as evidence:  “O you who?  Do not approach the PRAYER while you are intoxicated, so that you would know what you are saying, nor in a state of janabah, except if you passing-through, until you have performed ghusl.  And if you are ill, or on a journey, or one of you comes form the place of relieving oneself, or you have contacted women (in sexual intercourse) and do not find water, then wipe with clean earth over your faces and hands.  Indeed Allah is Pardoning and Forgiving.”

The argument used is that “prayer” means “place of prayer” or masjid, and that a junub may only pass through a masjid without sitting or sitting for a long time.

Correct Meaning

The Correct Meaning of this ayah is that it refers to those who become in a state of janabah while they are passing-through(i.e. traveling).  Such individuals may not pray until they have performed ghusl or tayammum.

 Another piece of evidence used is a hadith of Umm Atiyyah that the Prophet  commanded all women to go out for the id prayer and said:  “…And let those in menses stay away from the musalla (place of prayer)”

Correct Understanding

We know that the Prophet’s musalla was not a masjid.  It was an open land on the north side of the masjid used for id prayer, funeral prayers, animal sacrifices, and so on.  Thus, there is no reason to prevent anyone from entering it.  …the Phophet actually commanded the menstruating women to stay away from the prayer itself, even though they were present in the musalla grounds.

 The hadith, “I do not allow entering the masjid for a junub or a menstruating woman.”  However, this hadith is unauthentic because of Jasurah and other weak narrators in its chain.

 Evidence for the Permission:

   People Who Slept in the Masjid    Many reports of people sleeping in the masjid of the Prophet.  These included Ahl us-Saffah, men and women who perform i’tikaf, and the black woman who used to reside in the masjid.  It is conceivable that some of those would have wet dreams and become junub, and some of the women would menstruate.

 The Prophet indicated that she may enter the masjid because her menses is not in her control but in Allah’s control. …Once Allah’s messenger said to A’isha “Hand me the prayer mat from the masjid.”  She replied, “But I am in menses.”  He said:  “Indeed, your menses is not in your hand(control).”

   When A’isha menstruated during Hajj, the Prophet said to her: “Do what other pilgrims do, except for making tawaf around the House and praying –until you are clean.”

 Abu Hurayrah’s hadith that the Prophet “Exalted is Allah!  Indeed, a believe is never najis (filthy).”

   This provides a clear evidence that there is no grounds for prohibiting any believer from entering a masjid, because the reason for prohibiting any believer from entering a masjid, because the reason for prohibition is impurity or uncleanliness, as expressed in the ayah from at-Tawbah.

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