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Poliomyelitis is a highly infectious viral disease that causes lower limb paralysis in young children. The incidence rate of the diseases has persisted in some part of northern Nigeria despite the national and global effort to eradicate it. The study aims to describe the factors associated with polio vaccination non-compliance by some parents/guardians of targeted children in five high-risk wards of the study area. The study adopts a cross sectional qualitative study, conducted from 2014-2015, to gain insights into the factors associated with non-compliance to polio vaccination in high-risk wards in Bauchi LGA, Nigeria. 450 non-compliant houses were randomly selected for the study. The in-depth interviews consisted of 36 fathers and 18 mothers, while the key note interviews involved 18 Muslim clerics and 18 prominent traditional rulers, using semi-structured questionnaire. The results of the study revealed frequency or too many rounds of vaccine administrations; misconception/myth about the vaccine, migration, and child absence during immunization as reasons for non-compliance. Other factors include negative perception regarding the health and immunity status of the children, religious beliefs, while some of the respondent refused for no clear reason. It is therefore, essential to adopt programs that would enhance vaccine compliance; by for example, developing effective polio vaccines that can be administered at fewer visits to communities. Also, efficient health education needs to be conducted to enlighten the at-risk population, including special strategies targeting internally displaced and migrant populations.