We conducted a prospective, cross-sectional study to examine and compare treatment coverage of lymphatic filariasis by the health system (HST) and a health system implemented, community-directed treatment for the control of lymphatic filariasis (ComDT / HS) in 44 randomly selected villages in coastal Kenya. Demographic information on the villages and peripheral health facilities to guide design and implementation was obtained from a situation analysis phase of this study. A series of interactive training sessions on basic biology of lymphatic filariasis, concept and philosophy of ComDT / HS were given to members of the District Health Management Team (DHMT), peripheral health staff, community leaders and community drug distributors (CDDs) prior to ivermectin distribution. An intensive sensitization process of the community by the trained peripheral health staff and community leaders followed before selection of the CDDs. Quantitative and qualitative data for evaluation of the study were collected by coverage surveys of randomly selected households, focus group discussions and interviews, immediately after the drug distribution. Treatment coverage of all eligible persons was 46.5 and 88 % in HST and ComDT/HS villages, respectively, P < 0.001. In comparing treatment coverage by the two study arms in relationship to the distance from a health facility, coverage among HST and not ComDT / HS villages was influenced by distance. In Kenya, ComDT / HS can effectively be implemented by the regular health system and can attain coverage levels compatible with the global filariasis elimination goal.