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Substandard and falsified medicines represent a serious threat for public health and patient safety. Especially in low and middle-income countries, the prevalence of substandard and falsified medicines is reportedly high. However, reliable information on the prevalence of poor-quality medicines is scarce. In this study, 12 essential medicines, including antibiotics, antidiabetics, cardiac drugs and antiasthmatic drugs, were collected from six informal vendors and six licensed pharmacies in the southern part of Togo (regions Maritime and Plateaux). A mystery shopper approach was used in both types of outlets. In total, 64 samples were collected from licensed pharmacies and 30 from informal vendors. Both availability of medicines and prices of medicines were higher in licensed pharmacies than in informal vendors. 92 medicine samples were analyzed by visual examination, followed by chemical analysis for the content and for the dissolution of the active pharmaceutical ingredients according to the respective monographs of the United States Pharmacopoeia. 7 samples (8%) did not comply with the pharmacopoeial specifications, and one sample (1%) showed even extreme deviations. None of the samples was obviously falsified. However, one sample of amoxicillin capsules contained only 47% of the declared content of the active pharmaceutical ingredient, indicating that it may represent amoxicillin capsules 250 mg, rather than 500mg as declared on the label. Medicines stated to originate from Asia (i.e. mainly from India and China) showed a significantly higher proportion (24%) of non-compliant samples than those from Africa and Europe (4%, p = 0.007). High failure rates were observed in medicines both from informal vendors (13%) and from licensed pharmacies (5%), but the difference between both groups was not statistically significant (p = 0.152). The observed high prevalence of substandard medicines requires action from regulatory authorities and health care providers. Testing of selected samples for related substances indicated that inappropriate transport and storage conditions may have been an important cause for substandard quality., Competing Interests: The authors have declared that no competing interests exist.