Background: Quality data is a key element for every organization including the organization of the healthcare system. In fact, quality data allows any healthcare system to follow and evaluate the defined objectives in order to meet the needs of their customers. Therefore, it is necessary that the processes of producing these data are well structured and efficient. Unfortunately, in so many sub-Saharan African countries those processes have limits causing a qualitative issue in the collected data in the healthcare sector (for example, the low levels completeness, low levels of accuracy, low levels of promptitude) this is more and more frequent and it undermines the rightness of the intervention choices in the management of any healthcare system. Objective: To assess the level of performance of Gabon's health information system, we undertook to carry out an evaluation study of the processes used to collect quality data. Methods: This qualitative study was implemented using a five-step approach (identification of indicators in the data collection process, specification of data allowing the calculation of indicators, design of the data collection questionnaire, collection of data and health information system performance evaluation). For this assessment, we have chosen to rely on the characteristics (criteria) of three determinants that help ensure data quality (data recording and storage, verification of data accuracy and data processing and analysis). Results: It appears that 58% of the structures do not meet all the criteria that favor the recording and storage of data, 53% do not meet all the criteria that favor the verification of the accuracy of the data and 56% do not meet all the criteria that promote good data processing and analysis. Discussion: Although the dimensions used to assess the quality of the data in our study are not exhaustive, they nevertheless have the merit of describing and giving an idea of the level of performance of the healthcare information system in Gabon. Conclusion: We note from this study that Gabon's healthcare information system has limitations that do not allow it to produce reliable data to support strategic decisions and the results of this study may serve as material for reflection on the improvement of the current health information system.