Background: Federated learning methods offer the possibility of training machine learning models on privacy-sensitive data sets, which cannot be easily shared. Multiple regulations pose strict requirements on the storage and usage of healthcare data, leading to data being in silos (i.e. locked-in at healthcare facilities). The application of federated algorithms on these datasets could accelerate disease diagnostic, drug development, as well as improve patient care. Methods: We present an extensive evaluation of the impact of different federation and differential privacy techniques when training models on the open-source MIMIC-III dataset. We analyze a set of parameters influencing a federated model performance, namely data distribution (homogeneous and heterogeneous), communication strategies (communication rounds vs. local training epochs), federation strategies (FedAvg vs. FedProx). Furthermore, we assess and compare two differential privacy (DP) techniques during model training: a stochastic gradient descent-based differential privacy algorithm (DP-SGD), and a sparse vector differential privacy technique (DP-SVT). Results: Our experiments show that extreme data distributions across sites (imbalance either in the number of patients or the positive label ratios between sites) lead to a deterioration of model performance when trained using the FedAvg strategy. This issue is resolved when using FedProx with the use of appropriate hyperparameter tuning. Furthermore, the results show that both differential privacy techniques can reach model performances similar to those of models trained without DP, however at the expense of a large quantifiable privacy leakage. Conclusions: We evaluate empirically the benefits of two federation strategies and propose optimal strategies for the choice of parameters when using differential privacy techniques.