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Background  Health system weaknesses in Africa are broadly well known, constraining progress on reducing the burden of both communicable and non-communicable disease (Afr Health Monitor, Special issue, 2011, 14-24), and the key challenges in leadership, governance, health workforce, medical products, vaccines and technologies, information, finance and service delivery have been well described (Int Arch Med, 2008, 1:27). This paper uses focus group methodology to explore health worker perspectives on the challenges posed to integration of mental health into primary care by generic health system weakness.    Methods  Two ninety minute focus groups were conducted in Nyanza province, a poor agricultural region of Kenya, with 20 health workers drawn from a randomised controlled trial to evaluate the impact of a mental health training programme for primary care, 10 from the intervention group clinics where staff had received the training programme, and 10 health workers from the control group where staff had not received the training).    Results  These focus group discussions suggested that there are a number of generic health system weaknesses in Kenya which impact on the ability of health workers to care for clients with mental health problems and to implement new skills acquired during a mental health continuing professional development training programmes. These weaknesses include the medicine supply, health management information system, district level supervision to primary care clinics, the lack of attention to mental health in the national health sector targets, and especially its absence in district level targets, which results in the exclusion of mental health from such district level supervision as exists, and the lack of awareness in the district management team about mental health. The lack of mental health coverage included in HIV training courses experienced by the health workers was also striking, as was the intensive focus during district supervision on HIV to the detriment of other health issues.    Conclusion  Generic health system weaknesses in Kenya impact on efforts for horizontal integration of mental health into routine primary care practice, and greatly frustrate health worker efforts.  Improvement of medicine supplies, information systems, explicit inclusion of mental health in district level targets, management and supervision to primary care are likely to greatly improve primary care health worker effectiveness, and enable training programmes to be followed by better use in the field of newly acquired skills. A major lever for horizontal integration of mental health into the health system would be the inclusion of mental health in the national health sector reform strategy at community, primary care and district levels rather than just at the higher provincial and national levels, so that supportive supervision from the district level to primary care would become routine practice rather than very scarce activity.    Trial registration  Trial registration  ISRCTN 53515024

Health system challenges to integration of mental health delivery in primary care in Kenya- perspectives of primary care health workers