Background Pharmacogenomics describes inter-patient genetic variability in drug responses. Information based on whole genome sequencing will soon open up the field of pharmacogenomics, and facilitate the use of genomic information relating to drug metabolism and drug responses. We undertook a qualitative study, aiming to explore the potential barriers, opportunities and challenges facing the implementation of pharmacogenomics into primary care. Methods Semi-structured interviews were undertaken with 18 clinical participants (16 GPs and 2 other clinicians). All interviews were recorded and transcribed verbatim. Using a thematic analysis approach, data items were coded, ordered and themes constructed. Results Most participants were aged 55-60 years and worked as part-time clinical GPs with other clearly defined roles. The emerging themes covered several areas of concern, including: the utility of pharmacogenomics and the value of introducing such testing into primary care; how to educate the primary care workforce and ‘mainstream’ pharmacogenomics; the ethical, legal and social aspects of pharmacogenomics and its impact on patients; and potential impacts on the healthcare system particularly around economics and informatics.