Poor-quality medicines pose a significant challenge for health systems in low- to middle-income countries (LMICs),with recent deaths in multiple countries following ingestion of substandard cough syrups emphasising the need for quality-assurance of medicines in our increasingly interconnected global markets. Research also suggests that the source (country of manufacture) and type of medicine (generic/brand) are perceived to be associated with medicine quality. This study explores perceptions of medicines quality among national stakeholders of a medicines quality assurance system (MQAS) in sub-Saharan Africa. Through semi-structured interviews (n = 29) with managers from organisations responsible for the MQAS, public-sector doctors and nurses, and regulated private-sector pharmacists in three urban centres in Senegal in 2013. A thematic approach to analysis was undertaken with themes organised under three main categories, the source of drugs, the type of medicine, and medicines storage. A key emerging theme was the perception of the inferior quality of generic medicines, especially those produced in Asia and Africa, as they were lower in cost and thus believed to be less effective in alleviating symptoms than their brand versions. Medicines in Senegal’s less regulated (informal) street markets were also thought to be of poor-quality as they were not subjected to national regulatory processes or stored appropriately, resulting in exposure to direct sunlight and high temperatures. In contrast, the interviewees expressed confidence in medicines quality within the regulated sectors (public and private retail pharmacies) attributed to stringent national medicines regulation, secure medicines supply chains and adequate technical capacity to survey and analyse for medicines quality. Also, the views expressed typically described a medicine’s quality in terms of its effectiveness in alleviating the symptoms of ill health (efficacy of a medicine).These perceptions may have implications for developing national medicines policy, the procurement and supply of affordable medicines and consumers’ decision-making when purchasing medicines. Indeed, a proclivity for supplying and purchasing more expensive brand medicines may act as a barrier to accessing essential medicines.