Herbal products are used by human immunodeficiency virus (HIV)-infected individuals regardless of safety or efficacy concerns. In this study, we examined the microbiological quality of herbal preparations marketed to HIV-infected individuals. A convenience sample (N = 24) of herbal products was obtained from retailers in Nairobi, Kenya in 2007. Petrifilm plate count methods were used to estimate total aerobic bacteria (APC), coliform, Escherichia coli, Staphylococcus aureus and yeast and mould counts. APC counts ranged from an estimated 1.5 × 101 colony forming units (CFU)/g to 7.1 × 108 CFU/g. Total and faecal coliform counts ranged from an estimated <10 CFU/g to 3 × 106 CFU/g. E. coli load ranged from <10 CFU/g to 5 × 101 CFU/g and S. aureus counts ranged from an estimated <10 CFU/g to 2.5 × 103 CFU/g. Yeast and mould counts ranged from an estimated <10 CFU/g to 9 × 104 CFU/g. An evaluation using the World Health Organization limits for medicinal herbs found a percentage of samples to contain microorganisms above allowable limits: 33% (APC), 50% (coliforms) and 33% (yeast and moulds). A total of 67% of samples contained S. aureus loads above the United States Pharmacopeia standard. We suggest that the introduction of quality-control measures and safe handling practices for the selling of medicinal herbs and botanicals in Kenya would be beneficial in reducing the potential health risks for immunocompromised consumers of these products.