The effectiveness of information retrieval systems heavily depends on a large number of hyperparameters that need to be tuned. Hyperparameters range from the choice of different system components, e.g., stopword lists, stemming methods, or retrieval models, to model parameters, such as k1 and b in BM25, or the number of query expansion terms. Grid and random search, the dominant methods to search for the optimal system configuration, lack a search strategy that can guide them in the hyperparameter space. This makes them inefficient and ineffective. In this paper, we propose to use Bayesian Optimization to jointly search and optimize over the hyperparameter space. Bayesian Optimization, a sequential decision making method, suggests the next most promising configuration to be tested on the basis of the retrieval effectiveness of configurations that have been examined so far. To demonstrate the efficiency and effectiveness of Bayesian Optimization we conduct experiments on TREC collections, and show that Bayesian Optimization outperforms manual tuning, grid search and random search, both in terms of retrieval effectiveness of the configuration found, and in terms of efficiency in finding this configuration.