Successful interventions require consistent participation by intended recipients. We utilized mixed methods to describe participation of 518 parent-child dyads enrolled in a randomized cluster trial of a 2-year oral health intervention for Head Start (HS) families across Navajo Nation delivered by native Community Oral Health Specialists (COHS). We quantitatively assessed factors that contributed to participation and qualitatively examined barriers and strategies. The intervention offered fluoride varnish (FV) and oral health promotion (OHP) activities for two cohorts (enrolled in 2011, N = 286, or 2012, N = 232) of children in the HS classrooms and OHP for parents outside the classroom. Child participation was good: FV: 79.7 (Cohort 1) and 85.3 % (Cohort 2) received at least 3 of 4 applications; OHP: 74.5 (Cohort 1) and 78.4 % (Cohort 2) attended at least 3 of 5 events. Parent participation was low: 10.5 (Cohort 1) and 29.8 % (Cohort 2) attended at least three of four events. Analysis of survey data found significant effects on parent participation from fewer people in the household, Cohort 2 membership, greater external-locus of control, and a greater perception that barriers existed to following recommended oral health behaviors. Qualitative analysis of reports from native field staff, COHS, community members, and the research team identified barriers (e.g., geographic expanse, constraints of a research trial) and suggested strategies to improve parent participation (e.g., improve communication between COHS and parents/community). Many challenges to participation exist when conducting interventions in rural areas with underserved populations. Working with community partners to inform the development and delivery of interventions is critical. (author abstract)