Adoption of electronic health records (EHRs) is increasing worldwide. The worldwide EHR adoption rate is estimated to be around 9% to 12%. Thus, the accumulation of medical records in electronic form is also sharply increasing and is expected to be a precious asset for clinical research. Longitudinal observational studies based on EHRs are also increasing. Observational studies covering more than a million people are not rare at present. However, much of the current EHR data are equivalent in form to those of paper records, but are just stored in electronic stor-age devices, rather than as electronic data that can be transferred and shared without loss of clinical semantics. Current EHR systems must be improved in many ways to be used for anal-yses to yield important clinical knowledge. These improvements, which are addressed in this review, include the adoption of clinical data warehouses, use of controlled vocabulary, avoidance of personal/departmental research databases, a standardized interface of many diagnostic devices with the EHR system, control of time-stamp granularity, preparedness for whole-genome sequencing of every patient, confederation or consolidation of multi-institutional EHR data, protection of privacy and confidentiality, and an education system for clinical informaticians.