Deep convolutional neural networks require large amounts of labeled data samples. For many real-world applications, this is a major limitation which is commonly treated by augmentation methods. In this work, we address the problem of learning deep neural networks on small datasets. Our proposed architecture called ChimeraMix learns a data augmentation by generating compositions of instances. The generative model encodes images in pairs, combines the features guided by a mask, and creates new samples. For evaluation, all methods are trained from scratch without any additional data. Several experiments on benchmark datasets, e.g. ciFAIR-10, STL-10, and ciFAIR-100, demonstrate the superior performance of ChimeraMix compared to current state-of-the-art methods for classification on small datasets. Code is available at https://github.com/creinders/ChimeraMix.