Visual interpretation of electroencephalography (EEG) is time consuming, may lack objectivity, and is restricted to features detectable by a human. Computer-based approaches, especially deep learning, could potentially overcome these limitations. However, most deep learning studies focus on a specific question or a single pathology. Here we explore the potential of deep learning for EEG-based diagnostic and prognostic assessment of patients with acute consciousness impairment (ACI) of various etiologies. EEGs from 358 adults from a randomized controlled trial (CERTA, NCT03129438) were retrospectively analyzed. A convolutional neural network was used to predict the clinical outcome (based either on survival or on best cerebral performance category) and to determine the etiology (four diagnostic categories). The largest probability output served as marker for the confidence of the network in its prediction ("certainty factor"); we also systematically compared the predictions with raw EEG data, and used a visualization algorithm (Grad-CAM) to highlight discriminative patterns. When all patients were considered, the area under the receiver operating characteristic curve (AUC) was 0.721 for predicting survival and 0.703 for predicting the outcome based on best CPC; for patients with certainty factor ≥ 60 % the AUCs increased to 0.776 and 0.755 respectively; and for certainty factor ≥ 75 % to 0.852 and 0.879. The accuracy for predicting the etiology was 54.5 %; the accuracy increased to 67.7 %, 70.3 % and 84.1 % for patients with certainty factor of 50 %, 60 % and 75 % respectively. Visual analysis showed that the network learnt EEG patterns typically recognized by human experts, and suggested new criteria. This work demonstrates for the first time the potential of deep learning-based EEG analysis in critically ill patients with various etiologies of ACI. Certainty factor and post-hoc correlation of input data with prediction help to better characterize the method and pave the route for future implementations in clinical routine.