While there are many benefits associated with electronic prescribing, there are also a number of challenges associated with the implementation and ongoing maintenance of the systems. 

Funding. A concern for providers is the direct and indirect costs associated with implementing an e-prescribing system. All physicians, but particularly those in small practices, the inner city, or in rural settings, may believe that the cost of a system is too high for them to ever receive a positive return on investment (ROI). 

Change Management. To implement any health IT requires change management and new workflow systems. For the transition from paper to electronic prescriptions, this change can represent a very large hurdle.  Practices are used to doing things in a "certain way" and change can be difficult to get everyone one board (particularly those who are technology averse). Additionally, it can be very time-consuming to conduct the planning, training, and implementation of new electronic systems and workflows.

Hardware and Software Selection. Selecting the correct hardware, software, and post-implementation technical support for the practice environment can be difficult for many practices, including small or very busy offices or those that lack information technology staff. Practices often grapple with questions such as:

• Do they use a standalone system or one that is part of an electronic medical record?
• How do they select a vendor?
• How do they decide what the system needs to do?
• How do they implement it?
• Is the software certified ?

Connectivity: While almost all chain pharmacies (97 percent) are connected to the e-prescribing system, the vast majority (73 percent) of independent pharmacies are not yet connected.  Although most payers or PBMs (representing about 200 million lives) are connected, the patient, formulary, eligibility, or medication history information may not be current. 

Many small or rural providers and pharmacies face additional issues such as a lack of broadband connectivity and access to information technology professionals to support them. 

Standards: With the exception of the requirements (PDF - 209 KB) set forth by the Centers for Medicare and Medicaid Services (CMS) for use in Medicare Part D, there are no national standards for e-prescribing but they are being developed by the National Council for Prescription Drug Programs (NCPDP). While there are many organizations involved in the development and updating of e-prescribing and related technical standards for the reporting abilities, content and transmission, this work has not been harmonized across vendors and platforms.

State Regulations: There are variations in states about who may prescribe, what may be prescribed and under what circumstances. Reconciliation of those laws and requirements is important because many Americans live in one state and may obtain healthcare (including prescriptions) in another. State governments, such as Connecticut, need to conduct their own analysis of laws and regulations within their own states so as to update to accommodate e-prescribing, such as reconciling paper document retention requirements with electronic data storage, as well as facilitate e-prescribing and other health information exchange (such as remote monitoring and telemedicine) across state lines.

Controlled Substances: To date, the Drug Enforcement Administration (DEA) does not allow electronic transmission of controlled substances, which affects about 20 percent of prescriptions in the US. In July 2008, the DEA released proposed regulations (PDF - 384 KB) allowing e-prescribing of controlled substances for comment to the public (comments were due on September 25, 2008). Parallel to this effort, the DEA released the final rule (PDF - 232 KB) of the implementation of the Ryan Haight Online Pharmacy Protection Act of 2008 on April 6, 2009. The Department of Health and Human Services (HHS) is working with the DEA to promulgate regulations governing the issuance of a special registration to practitioners engaged in the practice of telemedicine. 

The following resources provide additional information on the challenges of e-prescribing:

• Identification of Backward Compatible Version of Adopted Standard for E–Prescribing and the Medicare Prescription Drug Program (NCPDP SCRIPT 10.6) Interim Final Rule - Released by the Centers for Medicare and Medicaid Services (2010).
• E-Prescribing Standards 101 - Developed by the National Council for Prescription Drug Programs (2011)
• Blueprint for e-prescribing: A Detailed Plan of Action for Implementing E-Prescribing  (PDF - 2.8 MB) - May 2008