Abstract: Artificial intelligence based diagnosis systems have emerged as powerful tools to reform traditional medical care. Each clinician now wants to have his own intelligent diagnostic partner to expand the range of services he can provide. When reading a clinical note, experts make inferences with relevant knowledge. However, medical knowledge appears to be heterogeneous, including structured and unstructured knowledge. Existing approaches are incapable of uniforming them well. Besides, the descriptions of clinical findings in clinical notes, which are reasoned to diagnosis, vary a lot for different diseases or patients. To address these problems, we propose a Medical Knowledge-enhanced Prompt Learning (MedKPL) model for diagnosis classification. First, to overcome the heterogeneity of knowledge, given the knowledge relevant to diagnosis, MedKPL extracts and normalizes the relevant knowledge into a prompt sequence. Then, MedKPL integrates the knowledge prompt with the clinical note into a designed prompt for representation. Therefore, MedKPL can integrate medical knowledge into the models to enhance diagnosis and effectively transfer learned diagnosis capacity to unseen diseases using alternating relevant disease knowledge. The experimental results on two medical datasets show that our method can obtain better medical text classification results and can perform better in transfer and few-shot settings among datasets of different diseases.