Transition from quantum to semiclassical behaviour and loss of quantum coherence for inhomogeneous perturbations generated from a non-vacuum initial state in the early Universe is considered in the Heisenberg and the Schrödinger representations, as well as using the Wigner function. We show explicitly that these three approaches lead to the same prediction in the limit of large squeezing (i.e. when the squeezing parameter |r k | → ∞): each two-modes quantum state (k, − k) of these perturbations is equivalent to a classical perturbation that has a stochastic amplitude, obeying a non-gaussian statistics which depends on the initial state, and that belongs to the quasi-isotropic mode (i.e. it possesses a fixed phase). The Wigner function is not everywhere positive for any finite r k , hence its interpretation as a classical distribution function in phase space is impossible without some coarse graining procedure. However, this does not affect the transition to semiclassical behaviour since the Wigner function becomes concentrated near a classical trajectory in phase space when |r k | → ∞ even without coarse graining. Deviations of the statistics of the perturbations in real space from a Gaussian one lie below the cosmic variance level for the N -particles initial states with N = N (|k|) but may be observable for other initial states without statistical isotropy or with correlations between different k modes. As a way to look for this effect, it is proposed to measure 0 the kurtosis of the angular fluctuations of the cosmic microwave background temperature.