Abstract Background As more integrative medicine educational content is integrated into conventional family medicine teaching, the need for effective evaluation strategies grows. Through the Integrative Family Medicine program, a six site pilot program of a four year residency training model combining integrative medicine and family medicine training, we have developed and tested a set of competency-based evaluation tools to assess residents' skills in integrative medicine history-taking and treatment planning. This paper presents the results from the implementation of direct observation and treatment plan evaluation tools, as well as the results of two Objective Structured Clinical Examinations (OSCEs) developed for the program. Methods The direct observation (DO) and treatment plan (TP) evaluation tools developed for the IFM program were implemented by faculty at each of the six sites during the PGY-4 year (n = 11 on DO and n = 8 on TP). The OSCE I was implemented first in 2005 (n = 6), revised and then implemented with a second class of IFM participants in 2006 (n = 7). OSCE II was implemented in fall 2005 with only one class of IFM participants (n = 6). Data from the initial implementation of these tools are described using descriptive statistics. Results Results from the implementation of these tools at the IFM sites suggest that we need more emphasis in our curriculum on incorporating spirituality into history-taking and treatment planning, and more training for IFM residents on effective assessment of readiness for change and strategies for delivering integrative medicine treatment recommendations. Focusing our OSCE assessment more narrowly on integrative medicine history-taking skills was much more effective in delineating strengths and weaknesses in our residents' performance than using the OSCE for both integrative and more basic communication competencies. Conclusion As these tools are refined further they will be of value both in improving our teaching in the IFM program and as competency-based evaluation resources for the expanding number of family medicine residency programs incorporating integrative medicine into their curriculum. The next stages of work on these instruments will involve establishing inter-rater reliability and defining more clearly the specific behaviors which we believe establish competency in the integrative medicine skills defined for the program.