To prevent diseases associated with inadequate sanitation and poor hygiene, people needing latrines and behavioural interventions must be identified. We compared two indicators that could be used to identify those people. Indicator 1 of household latrine coverage was a simple Yes/No response to the question “Does your household have a latrine?” Indicator 2 was more comprehensive, combining questions about defecation behaviour with observations of latrine conditions. Using a standardized procedure and questionnaire, trained research assistants collected data from 6,599 residents of 16 rural villages in Indonesia. Indicator 1 identified 30.3% as not having a household latrine, while Indicator 2 identified 56.0% as using unimproved sanitation. Indicator 2 thus identified an additional 1,710 people who were missed by Indicator 1. Those 1,710 people were of lower socioeconomic status (p < 0.001), and a smaller percentage practiced appropriate hand-washing (p < 0.02). These results show how a good indicator of need for sanitation and hygiene interventions can combine evidences of both access and use, from self-reports and objective observation. Such an indicator can inform decisions about sanitation-related interventions and about scaling deworming programmes up or down. Further, a comprehensive and locally relevant indicator allows improved targeting to those most in need of a hygiene-behaviour intervention.