The importance of primary health care (PHC) research is well understood yet conducting this research can be challenging. Barriers include a lack of funding, support and opportunity. In 2000 the Australian government introduced the Primary Health Care Research, Evaluation and Development (PHCRED) Strategy to address the gap in high-quality research. One component of the strategy, the Research Capacity Building Initiative, provided funding to university departments of general practice and rural health, allowing them to expand their pool of researchers and produce more research relevant to policy and practice. This study investigates the impact of phase two of the PHCRED Strategy by analysing peer-reviewed publications from PHCRED-supported departments. Research output was recorded from 2006 to 2010 incorporating 661 publications in 212 journals. Rural departments often had fewer resources than urban departments yet demonstrated steady research contributions focusing on issues relevant to their community. Since its inception the PHCRED Strategy has enabled development of research capacity and contributed to the body of PHC knowledge. While PHC is a diverse field, reflected in the publications produced, the themes underlying much of this work were representative of current health reform and the priority areas and building blocks of the National PHC Strategy.