Grazing-incidence small-angle X-ray scattering (GISAXS) has been used to study proteins embedded in thin polymer films obtained by a new cold, atmospheric-pressure plasma technique. In order to test the efficiency of the technology, four samples of alkaline phosphatase incorporated in organic polymer coatings in different plasma conditions have been investigated. Data have been analysed in the framework of the distorted-wave Born approximation (DWBA), by using a new method for the simultaneous fitting of the two-dimensional diffuse scattering from each sample. As a result, protein film concentration and aggregation state as well as a set of parameters describing the polymer coatings have been obtained. (C) 2008 Elsevier B.V. All rights reserved.