Introduction: Naturopathy is a mixture of both traditional and complementary medicine. It incorporates a broad set of health care practices that may or may not be traditional to that country or conventional medicine and are not fully integrated into the dominant health care system. Research required to evaluate or substantiate naturopathic medicine may not fall under the testing of randomized clinical trials, which opens up discussions on what is the best practice for research in naturopathic medicine.

Discussion: Not only do advances in health research methodology offer important opportunities to progress naturopathic research, there are also areas where the unique characteristics of naturopathic philosophy and practice can impact other areas of health research. Some of the new advances in health research methodology involve whole-system research, pragmatic trials, template for intervention description and replication protocols for complex interventions, patient-centered care models, and the pragmatic-explanatory continuum indicator summary tool for designing pragmatic trials. Discussion and critique of these health-related methodologies shows that these research methods are more suited for the philosophy and treatment options that naturopathy is based on.

Conclusions: Successful implementation of naturopathic research methodologies, and translation and dissemination of research will require a substantial paradigm shift in which naturopathic practitioners adopt a greater level of responsibility for developing an evidence base for naturopathic medicine.