Conclusions: This is among the first studies examining physician experiences transitioning between an older, locally developed EHR to a newer, commercial EHR with more robust CDS for e-prescribing. Understanding physician experiences with this type of transition and their general preferences for prescribing applications may lead to less disruptive system implementations and better designed EHRs that are more readily accepted by providers. In this way, productivity and safety benefits may be maximized while mitigating potential threats associated with transitions.Trial registration: ClinicalTrials.gov, Identifier: NCT00603070. (Source: International Journal of Medical Informatics).