BACKGROUND: The mental health system in Indonesia comprises attempts to modernise a colonial relic. There is still a disconnect between available services and help-seeking behaviours at the grassroots level. This study aims to explore the perceptions of Javanese people on the aetiology of mental illness and their ideas on how to deal with individuals who may have mental illness. METHODS: This qualitative study involves semi-structured interviews, embedded in a cluster randomised trial examining the clinical and cost-effectiveness of primary mental health services. Interviews were conducted with Indonesian and Javanese. The recruitment procedure was aligned to the trial. Participants were primary care patients recruited from 21 sites across Yogyakarta province. Interviews were recorded, transcribed, and translated into English. Thematic analysis was used to analyse the interview transcripts. RESULTS: 75 participants took part in the study: 51 women (68%) and 24 men (32%). Key themes emerged around perceived causes of mental health problems (including 'extrinsic factors'; 'intrinsic factors'; and 'spiritual factors'), and perceived appropriate pathways of care ('modern medical science'; 'social support and activities'; and 'religious or spiritual interventions'). Gender potentially influenced some of the responses. CONCLUSIONS: Themes indicate the variety of preconceptions towards mental health problems and assumptions regarding the best management pathways. Some of these preconceptions and assumptions support the utility of modern medical care, while the rest promote spiritual or religious healers. Participants' ideas of the appropriate care pathways largely correspond to their perception of what the symptoms are caused by. Despite hints to some understanding of the bio-psycho-social model of mental illness, most participants did not capture the complexity of mental health and illness, indicating the importance of contextual (especially culturally and religiously-aligned) public education around mental health, illness and care.