A method and system for anatomical object detection using marginal space deep neural networks is disclosed. The pose parameter space for an anatomical object is divided into a series of marginal search spaces with increasing dimensionality. A respective deep neural network is trained for each of the marginal search spaces, resulting in a series of trained deep neural networks. Each of the trained deep neural networks can evaluate hypotheses in a current parameter space using discriminative classification or a regression function. An anatomical object is detected in a medical image by sequentially applying the series of trained deep neural networks to the medical image.