It is estimated 350 million people worldwide are afflicted with a rare disease. Because each disease is different, there are significant challenges in obtaining enough information relevant to the patient’s condition to help inform diagnosis and treatment. While great strides have been made in exchange formats for sequence data, complementary standards for phenotypes and environment are urgently needed. Patient phenotypic abnormalities are currently described in diverse places in diverse formats: publications, public databases, electronic health records, clinical testing labs, disease registries, and social media. Here we propose a new standard for exchange of patient phenotype data that is optimized for integration from these distributed contexts. The PXF standard will allow phenotypic data to be captured at the point of publication, to be transmitted in the context of diagnostic testing, to be used for exchange of data in clinical studies, and as a backbone for patient-contributed data registries and social media. Increasing the volume of computable phenotype data across a diversity of systems will support large-scale computational disease analysis using combined genotype and phenotype data - something that patients themselves will now be able to participate in.