Abstract Phenotyping with electronic health records (EHR) has received much attention in recent years because the phenotyping opens a new way to discover clinically meaningful insights, such as disease progression and disease subtypes without human supervisions. In spite of its potential benefits, the complex nature of EHR often requires more sophisticated methodologies compared with traditional methods. Previous works on EHR-based phenotyping utilized unsupervised and supervised learning methods separately by independently detecting phenotypes and predicting medical risk scores. To improve EHR-based phenotyping by bridging the separated methods, we present Bayesian nonparametric collaborative topic Poisson factorization (BN-CTPF) that is the first nonparametric contentbased Poisson factorization and first application of jointly analyzing the phenotye topics and estimating the individual risk scores. BN-CTPF shows better performances in predicting the risk scores when we compared the model with previous matrix factorization and topic modeling methods including a Poisson factorization and its collaborative extensions. Also, BN-CTPF provides faceted views on the phenotype topics by patients’ demographics. Finally, we demonstrate a scalable stochastic variational inference algorithm by applying BN-CTPF to a national-scale EHR dataset.