Clinical researchers hold high expectations for the utility of health data sourced from hospital information systems. In Japan, the standardized structured medical information eXchange version 2 (SS-MIX2) storage is a common resource for obtaining clinical data from different medical databases. However, little is known about the coverage of the data types derived from the SS-MIX2 storage. In this regard, we calculated the proportions of a dataset that could be extracted via SS-MIX2 for various clinical study categories listed in various articles published in the New England Journal of Medicine. In the 95 articles reviewed, the proportions varied from 13.3% ± 13.3% (mean ± SD) for dementia to 61.8% ± 13.7% for diabetes. For cardiology, the proportion of data accessed in a unique format (SEAMAT) increased significantly. We further noted that there was room for improvement in the coverage of SS-MIX2 data.