There is something mysteriously seductive about the Yoga concept of Chakras and yet it is a topic that leads to a lot of confusion and misunderstanding.
1. Correct spelling
The word Chakra is better spelt without the 'h', i.e. Cakra, because that is the convention following the International Alphabet of Sanskrit Transliteration system that evolved from the 19th century.
I tell you this because I am about to drop my H-s and I wouldn't want you to think that my keyboard has got a lazy 'h' or that I am misspelling the perfectly correct Cakra.
Being more precise with spelling (and I am not the best speller or grammarian in the world) has its problems, viz. my auto-correct spellchecker wants to make "cakes" out of my "cakras".
We had better think about pronunciation while we are at getting the speeling right: it's pronounced more chuck-ra than chakra or shack-ra.
2. Origins and transmission
The Cakra model comes to us via haṭha-yoga sources, which sources were influenced by Tantric (tāntrika), and other, thinking.
Most of the material I looked at for this article were quite happy to tell me about the Cakra-s and related concepts, but refused to say where the ideas might have come from or how old they were. I think it is safe to say that the roots of the Cakra model go back a long way, that they started out as oral Indian tradition, evolved through use and interaction with other ideas before getting a mention in haṭha-yoga sources as already familiar and established systems.
There is an interesting Upaniṣad, the Praśna, which was probably composed in the second half of 1st millennium before Augustus Caesar (who was the first emperor of Rome about 2,000 years ago) and seems to anticipate the later theory of the cakra-s.
In the Praśna Upaniṣad we discover that four of the five different prāṇa-s (prāṇa can be thought of as our energy, vitality, life force, élan vital etc.) are based at specific points in the body: the throat, chest, navel and lower intestines .
Besides the obvious similarity as to the location of four of the main cakra-s we know today, we can't understand cakra theory without the central concept of prāṇa. In fact, there isn't much point to the cakra-s without prāṇa, and the channels prāṇa travels through (nāḍī-s).
TKV Desikachar explains that, from a haṭha-yoga point of view, human life is governed by prāṇa .
The "breath channels" (nāḍī-s) through which prāṇa travels are mentioned in the classical Upaniṣads like the Kaṭha (possibly composed in the second half of 1st millennium before Augustus Caesar): "101 channels (nāḍī-s) radiate from the heart but only one of them goes up to the crown of the head" says the Kaṭha (KU II.3.16).
3. The basics of Yoga's subtle anatomy
This is a heavy section; very abstruse stuff here even when simplified.
Haṭha-yoga appears to become a complete system of yoga by the end of the 11th century and by that time the nāḍī-s, cakra-s, and Kuṇḍalini are well established .
The cornerstone of haṭha-yoga practice is the breathing exercises known as prāṇāyāma.
Nothing is done in Yoga without reason or purpose. And we can say that the purpose of practising prāṇāyāma is to clean and balance the nāḍī-s. The nāḍī-s are the subtle channels of esoteric yoga physiology through which prāṇa flows. When practised with āsana (body postures), mantra-s (special sounds, words, phrases etc) and mudrā-s (bodily seals) it clears away the obstacle (Kuṇḍalini) that blocks prāṇa from entering the central channel known as suṣumṇā .
When, prāṇa enters the central channel, rises upwards and penetrates all the cakra-s, the goal of yoga (i.e. samādhi, where the mind becomes utterly still and able to discern the true difference between the world of energy-matter and pure consciousness) is reached.
Other yoga traditions see things differently: when prāṇa is forced into the central naḍi (the suṣumṇā) it awakens the dormant Kuṇḍalinī, which is sometimes represented as a serpent lying coiled at the base of the backbone where the nāḍī-s meet, or as the goddess Śakti, and it is Kuṇḍalinī that straightens out, rises upwards and penetrates all the cakra-s resulting in the attainment of haṭha-yoga's goal (samādhi).
According to the Haṭha Yoga Pradīpīkā ('HYP') (IV.8) there are 72,000 nāḍī-s. Of these 72,000 channels, three are considered very special and they are considered to lie close to each other following the line of the spine. They are the iḍā and piṅgala and running between them is the central channel/naḍi, the suṣumṇā.
The cakra-s (mystical circles or wheels; related to the Sanskrit root word "car" which means "to move") [sometimes known as padma-s (lotuses) or pīṭhas (mounds)] occur where these three major nāḍī-s are said to crisscross. Not all traditions agree that these three major nāḍī-s crisscross. Some prefer to conceive of the idā and the pingalā running up towards the nostrils on the left- and right-hand sides of the suṣumṇā, respectively.
The HYP tells us, in secretive language, that "when the sleeping Kuṇḍalinī awakens, then all the lotuses and knots are pierced. The central channel becomes the royal path of prāṇa. Then the mind is freed from all attachments to objects and Death is eluded" 
4. Real or symbolic?
There is a tendency to understand what's out there in terms of what we already believe.
We all do this. There have been some attempts to link the Cakra model to the endocrine glands (like the thyroid found in the throat), the neuro / autonomic plexuses (like the sympathetic nerve roots to the lungs and the heart), or to other organs (like the large intestines which terminates at the base of the torso) [4, 7].
I see these as attempts to unify two separate systems of thinking and to use one system to validate the other. This might not be wise.
As part of every yoga teachers' basic training is modern Western anatomy and physiology ('A&P'). A&P does not refer to Cakra-s . A&P is based, as you know, on empirical western evidence.
The explanation I like the best is the one that suggests that the Cakra model is a method for teaching and learning.
It enables a person to discover and learn something about themselves. They are a teaching aid to help the process of meditation [7, 9]. The commentary by Vyāsa on the Yoga Sūtra-s (III.1) says that "[meditation] consists in holding the mind on the navel circle, or the lotus of the heart, or on the [radiant] centre of the the head ..." 
Linked to experience through regular practice, the Cakra system becomes a powerful, albeit fictions or symbolic, educational method.
In a real sense the yogi makes her or his own cakra-s. The subtle body is a creation or a product of the yogic practice. If done well, it is a great help to the yogi. And every yogi should know that symbols can push us towards liberation but they can be traps that hold us back.
5. How many Cakra-s are there?
While the commonly held view in the West is that there are seven cakra-s, not all yoga and tantra authorities confirm this number.
The early Buddhist sources mention four Cakra-s, with later sources enlarging that number to five, six, seven, eight, nine, twelve and more Cakra-s [7, 8].
In his 1934 work, Yoga Makaranda, Krishnamacharya explains that there are ten Cakra-s in our body. They are the seven we are all familiar with plus the Sūrya-cakra, Manas-cakra and Brahma-guhā-cakra.
Most schools of Yoga and Tantra offer six Cakra-s with a seventh Cakra transcending the others . This gives us a six-plus-one Cakra model. The Cakra at the crown of the head (actually, the cranial vault might be a better description of the location), the sahasrāra, is not a Cakra like the others because only one nāḍī, the central one (i.e. the suṣumṇā), is associated with it. All the other six are closely associated with the three main nāḍī-s: the idā, pingalā and suṣumṇā. QED the seventh Cakra, isn't a Cakra, although it is very important.
6. The New Age stuff
I find it amazing how the Cakra system sucks up other ideas. Ascribing the colours of the rainbow and Jungian psychological insights to each cakra is very modern.
7. Srī T Krishnamacharya & TKV Desikachar
There are clearly different approaches to describing and working with Cakra-s.
In the Yoga Makaranda, Krishnamacharya placed a great deal of emphasis on the role of prāṇāyāma (breathing techniques).
Krishnamacharya and Deskichar's understanding of the cakra model was both authentic and practical. Desikachar tended note to teach much about the cakra-s becasuse they had more to do with tantra than with yoga. That said, their understanding :
emphasised the importance of prāṇa and the nāḍī-s (the pathways along which prāṇa - our life energy - flows)
draws attention to the idea that the cakra-s are places where prāṇa gathers and is reorganised
underlined how each cakra tells us something important about key areas of the body. For instance, our hips should have the quality of stability and that is why the energy of the mūlādhāra cakra, which is located at the base of the spine, is associated with the quality of earth (pṛthvī).
helps us notice that at the moment of death our prāṇa leaves us by following the specific route of the suṣumṇā and leaving via the sahasrāra cakra located at the crown of the head
includes the idea that the nāḍī and the cakra should be purified. In particular the main blockage in the yogi's subtle body is Kuṇḍalini. It is Kuṇḍalini that stops the haṭha yogi's inward attention reaching the deepest experience of the body, which experience lies along the spine.
emphasised that the cakra are points upon which the mind can focus
was applied practically during practice as a teaching and learning methodology. For instance, the seated forward bend, paścimatānāsana, done with adequate breathing will focus our attention on mūlādhāra cakra. Whereas the shoulderstand, sarvāṅgāsana, again done with an appropriate breathing pattern allows us to explore the viśuddhi cakra, located at the throat
empathised that an agitated and disturbed mind also means obstructed circulation of prāṇa and poor function of cakra-s
8. Summing up
One of the great things about yoga is that over the hundreds of years of its evolution it has collected everything that makes life easier, and every idea that reduces suffering.
The cakra-model is one of those ideas, and at its heart is Prāṇa and its close association with our minds (citta).
By working with and balancing the cakra-s, we balance the mind and when the mind is in harmony we can progress to the higher goal of yoga: freedom.
References and comments:
 Yogayājñavalkya Samhitā, IV.23-24, translated by TKV Desikichar and published by the Krishnamacharya Yoga Mandiram in 2000
 Haṭha Yoga Pradīpīkā, III.2-3
 The Upaniṣads, translated by Valerie J Roebuck and published by Penguin Books in 2003, see p. xxx
 Mark Olson, Ph.D., LMT, http://www.neurotrekker.com/anatomy/chakra2.pdf
 An article entitled, Śīrṣanana as a viparīta karaṇī mudrā, by TKV Desikachar, which appeared in KYM Darśanam magazine February 1994
 See for example: Steve Parker's 2009 book, The Concise Human Body or Leslie Kaminoff's 2007 book, Yoga Anatomy. However, Ray Long's 2005 book, The Key Muscles of Hatha Yoga, which omits the Cakra model when discussing the anatomy of yogāsana, does, however, include two brief (and not very useful) pages (of 230-odd pages) on Chakras.
 Georg Feuerstein, 1997, The Shambhala Encyclopedia of Yoga, p.67ff
 Gordon White, editor, 2012, Yoga in practice, p.14f
 Yoga Tārāvali, translated by TKV Desikachar and Kausthub Desikachar, published by the Krishnamacharya Yoga Mandiram in 2003, p.74ff
 Yoga Philosophy of Patañjali by Hariharānanda Āraṇya, rendered into English by P N Mukerji. This book was first published in 1963; my edition is (c) 1983, although I acquired my print much later.
 T Krishnamacharya, 1934, translated into English by TKV Desikachar and published by the Krishnamacharya Yoga Mandiram. I have the revised 2011 edition. See p.51ff