Analytic expressions for the mutual coherence function (MCF) and the scintillation index of a partially coherent lowest order Gaussian beam wave propagating through the atmosphere (based on Kolmogorov spectrum model) are developed for the pupil plane of a receiving system. Partial coherence of the beam is modeled as a thin (complex) phase screen with Gaussian spectrum (Rytov theory and ABCD ray matrices are applied). The relation between the second-and fourth-order statistics for a beam with any degree of coherence in the atmosphere is introduced with the help of ''effective'' beam parameters, deduced from the free-space MCF. In particular, the scintillation (in weak and strong atmospheric conditions), based on these parameters, is studied as a function of the diffuser's strength and that of the atmosphere. The model is applied for the calculation of the SNR and bit error rates (OOK modulation) of the communication link with diffuser at the transmitter and slow detection system. The improvement of bit error rates is observed in weak and strong atmospheric turbulence. In the weak regime, the optimal diffuser can be found. © 2004 Society of Photo-Optical Instrumentation Engineers.