Many patients attending general practice do not have an obvious diagnosis at presentation. Skills to deal with uncertainty are particularly important in general practice as undifferentiated and unorganised problems are a common challenge for general practitioners (GPs). This paper describes the management of uncertainty as an essential skill which should be included in educational programmes for both trainee and established GPs. Philosophers, psychologists and sociologists use different approaches to the conceptualisation of managing uncertainty. The literature on dealing with uncertainty focuses largely on identifying relevant evidence and decision making. Existing models of the consultation should be improved in order to understand consultations involving uncertainty. An alternative approach focusing on shared decision making and understanding the consultation from the patient's perspective is suggested. A good doctor-patient relationship is vital, creating trust and mutual respect, developed over time with good communication skills. Evidence-based medicine should be used, including discussion of probabilities where available. Trainers need to be aware of their own use of heuristics as they act as role models for trainees. Expression of feelings by trainees should be encouraged and acknowledged by trainers as a useful tool in dealing with uncertainty. Skills to deal with uncertainty should be regarded as quality improvement tools and included in educational programmes involving both trainee and established GPs.