BACKGROUND: The Global Programme to Eliminate Lymphatic Filariasis has set 2020 as a target to eliminate lymphatic filariasis (LF) as a public health problem through mass drug administration (MDA) to all eligible people living in endemic areas. To obtain a better understanding of compliance with LF treatment, a qualitative study using 43 in-depth interviews was carried out in Alor District, Indonesia to explore factors that motivate uptake of LF treatment, including the social and behavioural differences between compliant and non-compliant individuals. In this paper, we report on the findings specific to the role of family and gender relations and how they affect compliance. RESULTS: The sample comprised 21 men and 22 women; 24 complied with treatment while 19 did not. Gender relations emerged as a key theme in access, uptake and compliance with MDA. The view that the husband, as head of household, had the power, control, and in some cases the responsibility to influence whether his wife took the medication was common among both men and women. Gender also affected priorities for health care provision in the household as well as overall decision making regarding health in the household. Four models of responsibility for health decision making emerged: (i) responsibility resting primarily with the husband; (ii) responsibility resting primarily with the wife; (iii) responsibility shared equally by both husband and wife; and (iv) responsibility autonomously assumed by each individual for his or her own self, regardless of the course of action of the other spouse. CONCLUSIONS: (i) Gender relations and social hierarchy influence compliance with LF treatment because they inherently affect decisions taken within the household regarding health; (ii) health care interventions need to take account of the complexity of gender roles; (iii) the fact that women's power tends to be implicit and not overtly recognised in the household or the community has important implications for health care interventions; (iv) campaigns and other preventive interventions need to take account of the diversity of patterns of health care decision-making and responsibility in specific communities so that social mobilisation messages can be tailored appropriately.