OBJECTIVE: To investigate how physiotherapists prescribe execise for people with non-specific chronic low back pain in the absence of definitive or differential diagnoses. DESIGN: Four guided focus groups were conducted to gather the views of physiotherapists working in primary care. SUBJECTS AND SETTING: Twenty-three primary care physiotherapists from metropolitan Melbourne, Australia, were identified from professional organization member lists and publicly available records. They were recruited via email and assembled for focus groups based on eligibility, availability and location. MAIN MEASURES: Discussions were audio-taped, transcribed verbatim and analysed for themes by three independent researchers. RESULTS: The 'dilemma created by diagnostic uncertainty' emerged as a significant overarching theme with the following subthemes. Physiotherapists: (1) perceive that care-seekers want a clear diagnosis, (2) are challenged by diagnostic uncertainty, (3) are critical when patients fail to improve, (4) feel unprepared by traditional education models and (5) seek support from experienced colleagues. Physiotherapists report needing to: (1) educate care-seekers about their injury/diagnosis, despite diagnostic uncertainty, and (2)observe rapid health outcome improvements. They exhibit potentially negative behaviours, including blame attribution, when this does not occur. CONCLUSIONS: Physiotherapists appear under-prepared for the challenges of working with people with chronic conditions. Quality research is warranted to determine best practice in supporting practitioners in the development of suitable therapeutic behaviours to deal with this challenging patient interface.