Herbal products are used worldwide for the treatment and prevention of various diseases and currently represent a substantial proportion of the global drug market. However, these products have the potential of being contaminated by different microorganisms due to poor hygienic practices during handling, processing and packaging. The main aim of this study was to evaluate microbial quality of herbal products marketed to the general population in Eldoret and Mombasa, Kenya. The study employed an exploratory as well as laboratory based experimental design. The herbal products were purchased from the markets and transported to Kenya Medical Research Institute laboratories for processing and analysis. Microbial contaminants were determined according to Pharmacopoeias and World Health Organization standards. Microbial pathogens were isolated, identified and drug susceptibility test was done as per National Laboratory Standards Institute protocol. The herbal products were in-form of powders, liquids, tablets, oils and capsules. Bacterial contamination was observed in 90% of the total samples and those with >1000×10 4 cfu/gm or ml was 20% for Eldoret and 46% for Mombasa samples. Analysis of variance showed that the rate of microbial contaminants for Eldoret and Mombasa samples had no significant association (p = 0.084). Bacteria belonging to seven genera were isolated and antibiotic susceptibility test showed that 13.2% of the bacteria isolates were resistant. Multidrug resistance was observed with Klebsiella pneumonia, Shigella sonnei, Serratia erwinia, Serratia liquefaciens and Proteus penneri. These findings imply that conditions during harvest or postharvest processing of herbal products were unsanitary. Proper handling and storage of herbs should be observed in order to reduce the amount of microbial contaminants. Only 16% of herbal product samples evaluated met the standards for microbial limits as specified in Pharmacopoeias. Thus, emphasis on improvement of plant material quality and establishing better hygienic conditions during production of herbal medicines is recommended.