For the control of multiple new and resurgent diseases associated with microbial resistance to antimicrobials, there is renewed interest in using herbal medicines. However, the efficacy safety issues and good manufacturing practices associated with herbal medicines are major aspects to consider. The presence of pathogenic microorganisms in herbal medicines may adversely affect the therapeutic potential of the product or even make the product harmful to the patient. This study aimed to evaluate the hygienic quality and the microbiological hazard of herbal medicine produced and sold in city of Ouagadougou. Thus, a total of 45 samples of herbal medicines were collected randomly from the production sites of traditional practitioners and the various points of sale in Ouagadougou by herbalists. Research and enumeration of the total aerobic mesophilic flora, total coliforms, thermotolerant coliforms, yeasts, and some specific pathogenic bacteria such as Salmonella sp, Shigella sp, Staphylococcus aureus were performed according to methods based on standard procedures. Good manufacturing practices were also assessed through sample filtration on a 0.45 μm diameter filter and then a cloth sieve to detect physical contaminants. The results were interpreted according to European Pharmacopoeia standards and microbiological criteria for ready-to-eat meals. The results indicate an absence of Salmonella and Shigella. It was noted the presence of S. aureus (2.91.103 CFU/ml to 6.17.103 CFU/ml). The average loads of the different germs in the traditional medicines of the production and sales sites were respectively 1.26.106 and 4.36.106 CFU/ml for the total aerobic mesophilic flora, 0.88.105 and 1.78.105 CFU/ml for yeast and moulds, 0.34.104 and 1.22.104 CFU/ml for total coliforms, 1.14.103 CFU/ml and 4.15.103 CFU/ml for thermo tolerant coliforms. The search for physical contaminants revealed presence of sand, leaf pieces, and stems in some traditional medicines. In sum, this study demonstrated the presence of some pathogenic bacteria in some ready-to-use oral herbal medicines and lake of good manufacturing practices and hygienic conditions during the production chain. Given the importance of phytomedicines in health systems throughout the world and particularly in developing countries, it is necessary to train and sensitize producers of phytomedicines in good manufacturing practices and hygiene.