Trustworthiness is a major prerequisite for the safe application of opaque deep learning models in high-stakes domains like medicine. Understanding the decision-making process not only contributes to fostering trust but might also reveal previously unknown decision criteria of complex models that could advance the state of medical research. The discovery of decision-relevant concepts from black box models is a particularly challenging task. This study proposes Concept Discovery through Latent Diffusion-based Counterfactual Trajectories (CDCT), a novel three-step framework for concept discovery leveraging the superior image synthesis capabilities of diffusion models. In the first step, CDCT uses a Latent Diffusion Model (LDM) to generate a counterfactual trajectory dataset. This dataset is used to derive a disentangled representation of classification-relevant concepts using a Variational Autoencoder (VAE). Finally, a search algorithm is applied to identify relevant concepts in the disentangled latent space. The application of CDCT to a classifier trained on the largest public skin lesion dataset revealed not only the presence of several biases but also meaningful biomarkers. Moreover, the counterfactuals generated within CDCT show better FID scores than those produced by a previously established state-of-the-art method, while being 12 times more resource-efficient. Unsupervised concept discovery holds great potential for the application of trustworthy AI and the further development of human knowledge in various domains. CDCT represents a further step in this direction.