BACKGROUND: Health care seeking behaviour of households is influenced by individuals’ characteristics, type of diseases and access of health services. This study conducted to assess the health care seeking behavior and associated factors of urban and rural households for perceived morbidity in Southwest Ethiopia. METHODS: A comparative community based cross-sectional study was conducted among urban and rural households living in the Esera district, southwest Ethiopia. 377 head of households (119 urban and 258 rural dwellers), selected via simple random sampling technique after census, were the respondents. Healthcare seeking behavior on perceived illnesses of households of the district was assessed using a pretested structured questionnaire. Descriptive statistics, and binary and multiple logistic regression analysis were applied to compare and identify independent predictors of health care seeking behavior. RESULTS: A total of 377 (119 urban and 258 rural) households were included in the analysis making a response rate of 95.7%. Health care seeking behavior was higher among urban households (80.7%) than rural households (48.1%). Being married and perceived severity of disease were significantly associated with health care seeking behavior of urban households. Health seeking behavior of rural households was statistically different with monthly income, perceived severity of disease, acute duration of disease and distance from health facilities. CONCLUSIONS: The overall health seeking behaviors of households for perceived illness was satisfactory, but urban households seek health care more than rural. Health seeking behavior of urban households differed in matrimonial status and severity of disease perception, whereas, of rural households differed in household monthly income, severity of disease perception, duration of disease and distance from health center. This cues to work on accessibility and promotion of health care on the majority of the population of the country.