Hydrogen breath tests are a well-established method to help diagnose functional intestinal disorders such as carbohydrate malabsorption or small intestinal bacterial overgrowth. In this work we apply unsupervised machine learning techniques to analyze hydrogen breath test datasets. We propose a method that uses 26 internal cluster validation measures to determine a suitable number of clusters. In an induced external validation step we use a predefined categorization proposed by a medical expert. The results indicate that the majority of the considered internal validation indexes was not able to produce a reasonable clustering. Considering a predefined categorization performed by a medical expert, a novel shape-based method obtained the highest external validation measure in terms of adjusted rand index. The predefined clusterings constitute the basis of a supervised machine learning step that is part of our ongoing research.