We propose rectified factor networks (RFNs) to efficiently construct very sparse, non-linear, high-dimensional representations of the input. RFN models identify rare and small events, have a low interference between code units, have a small reconstruction error, and explain the data covariance structure. RFN learning is a generalized alternating minimization algorithm derived from the posterior regularization method which enforces non-negative and normalized posterior means. We proof convergence and correctness of the RFN learning algorithm.On benchmarks, RFNs are compared to other unsupervised methods like autoencoders, RBMs, factor analysis, ICA, and PCA. In contrast to previous sparse coding methods, RFNs yield sparser codes, capture the data's covariance structure more precisely, and have a significantly smaller reconstruction error. We test RFNs as pretraining technique of deep networks on different vision datasets, where RFNs were superior to RBMs and autoencoders. On gene expression data from two pharmaceutical drug discovery studies, RFNs detected small and rare gene modules that revealed highly relevant new biological insights which were so far missed by other unsupervised methods.RFN package for GPU/CPU is available at http://www.bioinf.jku.at/software/rfn.