BACKGROUND: Mass treatment to trachoma endemic communities is a critical part of the World Health Organization SAFE strategy. However, non-participation may not be at random, affecting coverage surveys and effectiveness if infection is differential. METHODOLOGY/PRINCIPAL FINDINGS: As part of the Partnership for Rapid Elimination of Trachoma (PRET), 32 communities in Tanzania, and 48 in The Gambia had a detailed census taken followed by mass treatment with azithromycin. The target coverage in each community was >80% of children ages <10 years. Community treatment assistants observed treatment and recorded compliance, thus coverage at the community, household, and individual level could be determined. Within each community, we determined the actual proportions of households where all, some, or none of the children were treated. Assuming the coverage in children <10 years of the community was as observed and non-participation was at random, we did 500 simulations to derive expected proportions of households where all, some, or none of the children were treated. Clustering of household treatment was detected comparing greater-than-expected proportions of households where none or all of children were treated, and the intraclass correlation (ICC) was calculated. Tanzanian and Gambian mass treatment coverages for children <10 years of age ranged from 82-100% and 62-99%, respectively. Clustering of households where all children were treated or no children were treated was greater than expected. Compared to model simulations, all Tanzanian communities and 44 of 48 (91.7%) Gambian communities had significantly higher proportions of households where all children were treated. Furthermore, 30 of 32 (93.8%) Tanzanian communities and 34 of 48 (70.8%) Gambian communities had a significantly elevated proportion of households compared to the expected proportion where no children were treated. The ICC for Tanzania was 0.77 (95% CI 0.74-0.81) and for The Gambia was 0.55 (95% CI 0.51-0.59). CONCLUSIONS/SIGNIFICANCE: In programs aiming for high coverage, complete compliance or non-compliance with mass treatment clusters within households. Non-compliance cannot be assumed to be at random.