In this paper we propose a highly accurate method of automatically estimation of the Gaussian noise level in digital images, which is based on image filtering and analysis of the region of interest. Noise level is an important parameter to many digital image processing applications, for example, when removing noise. As the noise level its standard deviation is calculated.  The selection of the noise component in an image is performed by high-pass filtration, where the Laplacian difference is used as the filter kernel. Based on the noise component of the image, regions of interest with homogeneous areas of the image are calculated. Region of interest are selected by the iterative method using low-pass filtration, where Gaussian two-dimensional function is used as the filter kernel. The noise level is calculated only in the regions of interest that contain almost no edges and textures, because edges and textures cause errors during the noise level estimation. In order to improve the accuracy of the method, edges of images are detected and out of region of interest. The high accuracy of the proposed method provides the use of high-pass and low-pass filtrations, iterative selection of region of interest and analysis of image edges. The accuracy of the developed method has been tested on the processing of 100 test images with different levels of software added Gaussian noise, as well as the processing of real photos with noise. The proposed method for the noise level estimation can be used for optimal automatic image filtering and for assessing the quality of photosensitive sensors.