We consider the problem of super-resolution from unregistered aliased images with unknown spatial scaling factors and shifts. Due to the limitation of pixel size in the image sensor, the sampling rate for each image is lower than the Nyquist rate of the scene. Thus, we have aliasing in captured images, which makes it hard to register the low-resolution images and then generate a high-resolution image. To work out this problem, we formulate it as a multichannel sam- pling and reconstruction problem with unknown parameters, spatial scaling factors and shifts. We can estimate the unknown parameters and then reconstruct the high-resolution image by solving a non- linear least square problem using the variable projection method. Experiments with synthesized 1-D signals and 2-D images show the effectiveness of the proposed algorithm.