A configurable toolkit for 3D/2D Convolutional Neural Networks (CNN). CNNs are used in Machine Learning to solve difficult classification and regression tasks. ELEKTRONN is based on Theano and benefits from fast GPU implementations. This toolkit was created by Marius Killinger and Gregor Urban at the Max Planck Institute For Medical Research For Medical Research to solve connectomics tasks. We provide a ready-made flexible training pipeline and comprehensive documentation.