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Pekalongan City is a filariasis endemic area in Central Java, Indonesia with Mf-rate >1%. It had held Mass Drug Administration (MDA) in 2011-2015. The evaluation result recommended it to re-hold MDA. This study aimed to compose filariasis vulnerability zonation based on environmental and behavioral aspects in Pekalongan City. The observed environmental aspects were the location of shrubs, cattle pen and tidal flood. The surveyed behavioral aspects were applicating mosquito repellent and hanging clothes habits. Filariasis cases data were collected from health office. This was a descriptive quantitative study with spatial approach. The environmental and behavioral aspects were observed and surveyed in 6 urban villages (38 RWs) with 387 households as samples which were chosen with proportional random sampling. The instruments were checklist sheets, Global Positioning System (GPS), satellite imagery and GIS software. Data were analyzed with scoring, buffering and overlaying procedures. Results indicated some areas were categorized as highly vulnerable where shrubs, cattle pen, tidal flood and hanging clothes habit were present. It was concluded that all urban villages in this study had highly vulnerable RWs which are very potential for filariasis transmission. Applicating mosquito repellent habit was not potential aspect for controlling filariasis transmission in the studied areas.