Methods of detecting relative misalignment between a color filter array and a sensor array in a color sensor array. The present invention provides methods for detecting and compensating for shifts of one or more rows and/or columns between a color filter array and a sensor array that may occur during the color sensor array fabrication process. The present invention also enables the use of color sensor arrays in which the alignment of a color filter array relative to the corresponding sensor array is unknown. In one embodiment, a detectable pattern of one or more pixels (e.g., pixels having black filters) is introduced into the periphery of the color sensor array. The position of the pattern is detected and color image data are processed with respect to the detected position. The invention is very cost effective and enables the use of image sensors with misaligned color filter arrays just as if they were manufactured correctly. The benefits of the present invention include (1) increased manufacturing yields and, therefore, lower per unit manufacturing cost and (2) higher reliability of image sensors configured with color filter arrays.