Qur'an is organized with respect to the location of revelation of verses, whether in Makkah or Madinah. The part of the Qur'an that was revealed in Makkah, almost two-third, carries the title, Makki and remainder carries the title Madani. Makki part emphasizes belief of Tawheed (Islamic monotheism), Risalah (guidance of mankind through Allah's selected prophets and messengers) and Aakhira (destruction of this world and the life hereafter that includes physical and spiritual resurrection of humankind, the day of judgment and the life of paradise or hell) whereas the Madani part emphasizes Ibadat (servitude to Allah) andMu'amilat (all aspects of relationship with other beings). Many scholars look at the content of verses and can speculate whether it was revealed in Makkah or Madinah. For example, qital (one aspect of jihad) was ordained in Madinah whereas in the Makki period emphasis was on keeping the hands tied in face of adversity and persecution. Similarly, orders of Zakat (wealth cleansing tax), Hudood (legally defined crimes and their punishment) and Hajj (pilgrimage to Makkah) were revealed in Madinah.
Qur'an has words, ayahs (verses) and Surahs (chapters). Scholars have taken the time to count the number of letters and words but it is not relevant to our study. Those who are interested can find information about letters and words in the books about the Qur'an.
The Qur'an is divided into Ayahs or signs, commonly translated as verses. An ayah may consist of a full sentence more than one sentence or part of a sentence. What makes an ayah is revealed knowledge not a decision of the Prophet Muhammad or any scholar. The sequence of appearance of ayat is also revealed knowledge. Ayahs may be Makki or Madani but in the opinion of some scholars, some ayah may consist of a part Madani and another part Makki; an example is the last verse of Surah Muzammil. The Qur'an has approximately 6,300 ayat. Due to various conventions used there is a slight discrepancy in counting the total number of ayat. For example, according to one convention Surah Al-Fatiha has seven ayahs that includes Bismillah and another convention the seven ayat excludes Bismillah. One convention includes 113 Bismillah as part of chapters and the other convention excludes it.
A group of ayat has been declared to make up a Surah. Surahs vary in length, shortest ones have only three ayahs and the longest one has 286. There are 114 Surahs in the Qur'an numbered from 1 to 114. Surah means something divided or walled from both sides. All Surahs begin with Bismillah except Surah No. 9 called At-Taubah or the Repentance. All Surahs have been divided into Makki and Madani but a Makki Surah may contain a few verses revealed in Madinah and vice versa. There are some differences of opinion among the scholars of the Qur'an regarding the place of revelation of a few verses and their inclusion into a given Surah. All Surahs have been given names but not titles. A title is a brief, one word or two words description of the contents but name is not a description. For example, the name John or Yahya does not describe anything about this person but Dr. Yahya has a title Doctor describing his education. Similarly, names of Surahs like Al-Baqarah (the Cow) or Al-Ankaboot (the Spider) are not titles of those Surahs but only names. If they were titles, the Surah would be about the cow and spider, respectively. However, in some rare cases a name of a Surah may also be its title, such as Surah Yusuf.
The most scientific method is the one given to us by the Prophet Muhammad, that is Surah and verse. Since all Surahs and ayat within them are numbered, the most scientific method is to provide the Surah and ayah number. For example Ayat al-Kursi is 2:255, that is Surah 2 (Al-Baqarah) and ayah 255. Some scholars prefer the reference Al-Baqarah 255 or Al-Baqarah (2): 255.
The organization of ayat and Surah and their order is revealed by Allah to His Prophet.
Scholars after the Prophet have done additional division of the Qur'an for the convenience of recitation of the whole Qur'an in a set period like one week, one month or two months and so on.
The Qur'an is divided into seven approximately equal parts for the convenience of reciting the whole Qur'an in one week. Each of the seven parts is called Manzil or station or the plural is Manazil or stations. There is some indication that Prophet Muhammad may have suggested such a division but there is no definite proof of it. A Manzil (singular of Manazil) consists of a number of whole Surahs as given below. If we take Surah 1 as preface of the Qur'an and exclude it from the seven Manazil, the division of Manazil follows:
Manzil No. 1. Surahs 2, 3 and 4.
Manzil No. 2. Surahs 5 to 9.
Manzil No. 3. Surahs 10 to 16.
Manzil No. 4. Surahs 17 to 25.
Manzil No. 5. Surahs 26 to 36.
Manzil No. 6. Surahs 37 to 49.
Manzil No. 7. Surahs 50 to 114.
In South Asia, Juz is also called Para. The Qur'an was equally divided into thirty parts, perhaps based on the number of pages disregarding content or Surah. This was done for the convenience of reciting the whole Qur'an in thirty days or one month. Each Juz is also divided into four quarters or four ruba. The Qur'an copies printed anywhere in the world have Juz and quarter markings as ruba' (first quarter), nusf (one-half) and al-thulatha (three-quarter). This gives 120 quarter-parts of the Qur'an giving the flexibility of reciting the whole Qur'an in equal parts in 30, 60 or 120 days. This type of partitioning of the Qur'an is used very much in South Asia whereas the Arab world does not make much use of it. Even referring to Qur'anic verses South Asians would talk in terms of Para number as they carry numbers from 1 to 30 for each Juz. This kind of referring to the Qur'an verses is very unscientific because it does not provide precise location of the verse. If someone says that a verse is in 15th Para , it is not precise enough to find it easily.
According to this system each Juz is further divided into two Hizbs and each Hizb is further divided into four quarters. It means that a Juz has two Hizbs and eight Hizb-quarters or each Juz-quarter has two Hizb-quarters. The whole Qur'an is divided into 240 Hizb-quarters. This allows a person to recite the Qur'an in small groups of verses and complete the recitation in one-month to eight-month period. In addition, Hizb partitioning of the Qur'an allows a Muqri (Qur'an reciter) to recite one Hizb in each Raka'ah of Salat at-Traweeh and finish one Juz every night in eight Raka'hs thereby completing the whole Qur'an in 30 nights of Ramadan. Partitioning of the Qur'an in Hizb is not found in the copies printed in South Asia .
Some Muslims prefer to do 20 raka'ah every night for Salat At-Taraweeh during the month of Ramadan, that is, recite a section and go to ruku' (bowing). They had to find markers to recite a portion of the Qur'an in each Raka'ah while completing a topic. In South Asia the tradition is to complete recitation of the whole Qur'an in 27 nights. This required partitioning of the Qur'an in 27 x 20 = 540 sections excepting the Surah al-Fatiha. When such partitioning was done they ended up with 556 (+1 for Surat al-Fatiha) sections. Evidently, they did not go back to redo the partitioning to come with 540 sections. The Qur'an copies printed in South Asia have Ruku' or Section markings showing number of the ruku' within the Surah, within the Juz and ayah number within the ruku'. Traditionally, South Asian Muslims may give reference of a ayahs from the Qur'an by referring to the ruku' number and Juz number but such system is unscientific and it is not universally acceptable. Qur'an copies printed in the Arab world do not include ruku' markings.
Some Qur'an scholars talk in terms of groups of Surah or complementary couples of Surahs. These complementary groups or couples are based on the themes and like contents. For example, there is a group of Musabbihat, five Surahs that begin with glorification of Allah ( Sabbah lillahi or Yusabbihu lillahi ). There are many other groups of Surahs that have been suggested. Also, there are twins or complementary couples, such as Surahs 2 and 3 make a couple, Surahs 91 and 92 is another couple. According to such scholars most of the Qur'an consists of complementary couples.