The cosmic microwave background radiation appears to us to be not quite uniform in temperature or intensity in all directions; that is, it is not isotropic. Why is this?
I don't think this is a perfect answer, let's just say it's ok as a first approximation.
In the very early universe (and I mean billionths of billionths of a second) the Universe was, obviously, much smaller. At this scale quantum physics was dominant and there were random fluctuations in density and 'temperature'.
These variations were flattened out, but not removed, by the process of inflation which saw the Universe expand explosively in a fraction of a second. This is used to explain the remarkable similarity in the temperature of the cosmic microwave background radiation (CMBR).
The variations which we see are really very tiny, less than one part in 10 000, but still require explanation and quantum physics followed by inflation seems to be the best explanation we have to date.