The need for research to conform to recognized ethical standards while the dignity, rights, safety and welfare of vulnerable individual are protected necessitates the adequate functioning Health Research Ethics Committee (HREC). This study therefore investigated the factors influencing the work of HREC in Bauchi and Sokoto States, Nigeria. The study is a cross sectional survey of ethics committee members between 2014 to 2015. In dept interview were separately conducted for each of the six active HRECs members recruited from each state in this study. Prior to the conduct of the interview, informed consent and appointment for the face to face interview were earlier sought and granted by the respondents. Respondents admitted that there was no oversight function in the role of HREC to review and approve the research protocols. The ethical protocols take between two weeks to a month before approval. Although, members of committee showed record of good attendance but their performance was rated average while the quarterly scheduled meeting has not been consistent. More so, there has not been any rotation of the members of committee since the inception of the body. However, all the respondents agreed that they have been receiving quality training mostly sponsored by TSHIP. Despite non-financial gains respondents offered voluntary services. The challenges commonly encountered by the HREC committee includes non-availability of an office, office equipment and stationeries, challenges in the monitoring of research work and lack of budgetary allocation for the committee for refreshment during meetings. Operations of HREC committees in Bauchi and Sokoto States have enhanced the research activities in the states. However, inclusion of more academicians as reviewers and support of state governments is very essential for the improved performances of the committees.