There are a two primary categories of the EMR; the "born digital" record and the scanned/imaged record.

The "born digital" record, which is information captured in a native electronic format originally is information that may be entered into a database, transcribed from an electronic tablet or notebook PC, or in some other manner captured from its inception electronically. The information is then transferred to a server or other host environment, where it is stored electronically.

The second category are records originally produced in a paper or other hardcopy form (x-ray film, photographs, etc.) that have been scanned or imaged and converted to a digital form. These records are best described as "digital format records", as their content is not able to be modified or altered (with the exception of the use of a third party software to make "overlay notations") as electronic records are. Most medical records generated preceding the year 2000 are of this category.

The process involved in conversion of these physical records to EMR is an expensive, time-consuming process, which must be done to exacting standards to ensure exact and accurate capture of the content. Because many of these records involve extensive handwritten content, some of which may have been generated by any number of healthcare professionals over the life span of the patient, there exists a high probability of some of the content being illegible following conversion. In addition, the material may exist in any number of formats, sizes, media types and qualities, which further complicates accurate conversion. Consideration should be given to developing a procedure to sample and verify images at a high ratio to determine the accuracy and usability of the scanned images prior to disposal of the physical records, if they are disposed of at all.

Further, all electronic repositories of information are subject to the need for periodic conversion and migration to ensure the formats they were captured in remain accessible over the life of the patient, and in some cases beyond, to the expected life of their heirs. Additionally, those responsible for the management of the EMR are responsible to see the hardware, software (applications) and media used to manage the information remain viable and are not subject to obsolecense or degradation. This will require generation of backup copies of the data and protection being provided to these copies in the event of damage to the primary repository. It will also require the planned periodic migration of information to address concerns of media degradation from use. These are all costly, time consuming processes that must be planned and budgeted for when making decisions to convert physical medical records to digital formats.

Another major concern is adequate protection of privacy of the individuals whose records are being managed electronically. This class of information (in the US) is referred to as Personal Healthcare Information (PHI) and its management is addressed under the Healthcare Insurance Portability and Accountability Act (HIPAA) as well as many State-specific privacy laws. The organization/individuals charged with the management of this information are required to ensure adequate protection is provided and that access to the information is only by authorized parties.