Autoencoders have been recently used for encoding medical images. In this study, we design and validate a new framework for retrieving medical images by classifying Radon projections, compressed in the deepest layer of an autoencoder. As the autoencoder reduces the dimensionality, a multilayer perceptron (MLP) can be employed to classify the images. The integration of MLP promotes a rather shallow learning architecture which makes the training faster. We conducted a comparative study to examine the capabilities of autoencoders for different inputs such as raw images, Histogram of Oriented Gradients (HOG) and normalized Radon projections. Our framework is benchmarked on IRMA dataset containing 14,410 x-ray images distributed across 57 different classes. Experiments show an IRMA error of 313 (equivalent to ≈ 82% accuracy) outperforming state-of-the-art works on retrieval from IRMA dataset using autoencoders.