Abstract Background Primary care doctors in NHSScotland have been using electronic medical records within their practices routinely for many years. The Scottish Health Executive eHealth strategy (2008-2011) has recently brought radical changes to the primary care computing landscape in Scotland: an information system (GPASS) which was provided free-of-charge by NHSScotland to a majority of GP practices has now been replaced by systems provided by two approved commercial providers. The transition to new electronic medical records had to be completed nationally across all health-boards by March 2012. Methods We carried out 25 in-depth semi-structured interviews with primary care doctors to elucidate GPs’ perspectives on their practice information systems and collect more general information on management processes in the patient surgical pathway in NHSScotland. We undertook a thematic analysis of interviewees’ responses, using Normalisation Process Theory as the underpinning conceptual framework. Results The majority of GPs’ interviewed considered that electronic medical records are an integral and essential element of their work during the consultation, playing a key role in facilitating integrated and continuity of care for patients and making clinical information more accessible. However, GPs expressed a number of reservations about various system functionalities – for example: in relation to usability, system navigation and information visualisation. Conclusion Our study highlights that while electronic information systems are perceived as having important benefits, there remains substantial scope to improve GPs’ interaction and overall satisfaction with these systems. Iterative user-centred improvements combined with additional training in the use of technology would promote an increased understanding, familiarity and command of the range of functionalities of electronic medical records among primary care doctors.