Patient uncertainty is associated with conditions with no known cause or cure, such as systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA), and despite its potential role in chronic illness management, it is still a poorly understood concept. This study constitutes an in-depth investigation of patient uncertainty in SLE and RA. We conducted (i) structured interviews with a sample of rheumatology health care professionals (HCPs) (n = 8) and (ii) in-depth, semi-structured interviews with a sample of SLE (n = 17) and RA (n = 15) patients. Interviews were audio-taped, transcribed verbatim and analysed thematically using detailed line-by-line coding. Patient uncertainty was conceptualised in a framework of five domains: symptoms and prognosis, medical management, self-management, impact and social functioning. Even though these five domains were present in both the SLE and RA data, there were some differences at the sub-domain level. Several sources of uncertainty were put forward by the HCPs and subsequently confirmed in the patient interviews including the illness trajectory, age, gender and timing. Patients reported uncertainty relative to various aspects of their illness, its management and impact. Finally, HCPs discussed the behavioural and psychosocial impact of uncertainty, which further suggests its important role in patient management.