High-throughput microscopy generates a massive amount of images that enables the identification of bio- logical phenotypes resulting from thousands of different genetic or pharmacological perturbations. However, the size of the data sets generated by these studies makes it almost impossible to provide detailed image annotations, e.g. by object bounding box. Furthermore, the variability in cellular responses often results in weak phenotypes that only manifest in a subpopulation of cells. To overcome the burden of providing object-level annotations we propose a deep learning approach that can detect the presence or absence ofrare cellular phenotypes from weak annotations. Although, no localization information is provided we demonstrate that our Weakly Supervised Convolutional Neural Network (WSCNN) can reliably estimate the location of the identified rare events. Results on synthetic data set and a data set containing genetically perturbed cells demonstrate the power ofour proposed approach.