What is the origin of CMB fluctuations? I have read somewhere that CMB (cosmic microwave background radiation) fluctuations in temperature are linked to mass distribution fluctuations in the early universe (at ~350000 years after Big Bang, which is of course when the cosmic radiation was emitted), and that is used to explain the formation of large structures (galaxies, clusters of galaxies..). Why is that so?
 A: 
The CMB  (cosmic microwave background) is a snapshot of the oldest light in our Universe, imprinted on the sky when the Universe was just 380,000 years old. It shows tiny temperature fluctuations that correspond to regions of slightly different densities, representing the seeds of all future structure: the stars and galaxies of today.


The anisotropies are very small,

The cosmic microwave background radiation is an emission of uniform, black body thermal energy coming from all parts of the sky. The radiation is isotropic to roughly one part in 100,000: the root mean square variations are only 18 µK, after subtracting out a dipole anisotropy from the Doppler shift of the background radiation .

One needs a model and the dominant one is the Big Bang model 

This light stopped interacting with electrons and nucleons at 380.000 years after the BB,
before gravitational attraction formed stars and galaxies. The great uniformity of temperatures, at the level of 10^-5, cannot be explained thermodynamically because there was no uniform communication over the then universe ( due to special relativity) of the particles and energy forms before the photon separation, to homogenize the soup.  This uniformity forced the inflation period in the very beginning of the Big Bang model. The rapid inflation homogenized the primordial soup so that we end up with the observed CMB spectrum.
The CMB has been used to model a homogeneous early inflation period to explain  the CMB observation. Once the CMB homogeneity was  modeled  by the inflationary period, the homogeneity in the density of  cluster of galaxies and galaxies  also follows.

and that is used to explain the formation of large structures (galaxies, clusters of galaxies..).

The CMB does not explain the formation of large structures, those are explained by statistical mechanics and gravitational forces as the universe cooled from the BB . It explains the homogeneity  , which is still under study.
A: The CMB is a snapshot of the state of the universe at the moment when the universe cooled enough to allow protons to capture electrons to form atoms, thereby allowing light to travel unimpeded for the first time - prior to this the universe was a remarkably uniform distribution of plasma.  But there -were- minute variations, which appear to be a Gaussian random field: http://en.wikipedia.org/wiki/Gaussian_random_field ).  The hotter spots reveal regions of slightly higher density, so it's theorized that these became centers of gravity for stars/galaxies to coalesce.  This gives us a starting point to map the evolution of the universe over time to the present era.
