Natural language processing (NLP) engines such as the clinical Text Analysis and Knowledge Extraction System are a solution for processing notes for research, but optimizing their performance for a clinical data warehouse remains a challenge. We aim to develop a high throughput NLP architecture using the clinical Text Analysis and Knowledge Extraction System and present a predictive model use case.The CDW was comprised of 1 103 038 patients across 10 years. The architecture was constructed using the Hadoop data repository for source data and 3 large-scale symmetric processing servers for NLP. Each named entity mention in a clinical document was mapped to the Unified Medical Language System concept unique identifier (CUI).The NLP architecture processed 83 867 802 clinical documents in 13.33 days and produced 37 721 886 606 CUIs across 8 standardized medical vocabularies. Performance of the architecture exceeded 500 000 documents per hour across 30 parallel instances of the clinical Text Analysis and Knowledge Extraction System including 10 instances dedicated to documents greater than 20 000 bytes. In a use-case example for predicting 30-day hospital readmission, a CUI-based model had similar discrimination to n-grams with an area under the curve receiver operating characteristic of 0.75 (95% CI, 0.74-0.76).Our health system's high throughput NLP architecture may serve as a benchmark for large-scale clinical research using a CUI-based approach.