Introduction: The importance of health research in addressing equity, health outcomes and development is recognised by world leaders and yet there is a lack of research outputs from low to middle income countries, such as those in the Pacific Islands, where the burden of disease is higher. A lack of research generation and utilisation is a manifestation of under-developed health research systems that are in turn built on underfunded and under-resourced health systems. A lack of researchers, lack of research skills and poorly developed national health research systems are the main reasons for the lack of research output and yet common to all countries is a clinical workforce, that, despite heavy clinical workloads, are interested in performing clinical research and audit. Research workshops despite differing objectives, duration and curriculums have been shown to increase research knowledge and other research outputs such as publications. What is not known is whether a one-off research workshop and mentoring would increase the research productivity of clinicians in the Pacific. The aims of this study were to determine the effectiveness of a standalone research workshop and mentoring on the clinicians’ research performance and develop a tool for assessing clinician research outputs in resource-poor countries. Methods A survey of health research systems in six Pacific countries was conducted in Fiji, Samoa, Cook Islands, Solomon Islands, Vanuatu and Tonga. Another survey was conducted into research needs in the whole region. Twenty-eight clinician leaders were recruited with different backgrounds from the six Pacific Island countries to attend a six-day research workshop. The workshop was held in Auckland and most of the teaching faculty were from the University of Auckland. The participants’ characteristics and views about research performance measures were examined by a series of surveys, interviews and focus group discussions. They were supported with one-to-one and group mentoring via social media sites or other means to complete identified research and clinical audit projects. A Delphi survey of 19 research experts identified factors that together with the clinician participants’ opinions informed the development of a research performance tool for the Pacific setting that was used to assess the participants’ performance at 18 months after the research workshop. Findings The national health research systems in the six countries were at varying stages of development with improvements in the seven years since a similar survey was used especially in Fiji, the Cook Islands, Solomon Islands and Samoa. There was a regression in development in Vanuatu and Tonga. There were 174 reproductive health papers published from 14 Pacific countries and territories over 12 years to 2011 and most of them (57%) were from Papua New Guinea where there are several academic institutions including a well-funded medical institute with international collaborations. The research workshop increased the knowledge, motivation and enthusiasm of the clinicians in research. Research collaboration and implementation were considered preferred measures of research productivity in the low resource setting. Not all the clinicians utilised the mentors assigned them and the group mentoring on the social media sites were under-utilised. Of the 18 clinicians who completed the assessment, 7 were considered research successful and most were medical specialists and academics. Conclusion A stand-alone workshop and mentoring were modestly successful in increasing research activity in the Pacific Islands. Health research systems need strengthening through the development of national academic institutions and collaborative regionalism. Research outputs and outcomes can be improved within countries by focusing on long-term goals in research training, support and collaborations. Long term success in achieving departmental and institutional research goals can only be achieved where there is a critical mass of clinicians in teams performing research with enabling policies of a health research system and collaborations for funding and skills.