This study aimed to monitor microbial contamination levels in a variety of health functional foods and to establish new microbial criteria. Indicator organisms (i.e., aerobic bacteria, coliform bacteria, and Escherichia coli) were monitored in 10 health functional food categories (743 items, 3,715 samples). The mean total aerobic counts of ginseng and Korean red ginseng were −0.35 and −0.74 log CFU/g; and the mean total coliform counts were −1.4 and −1.39 log CFU/g, respectively. In addition, the mean total coliform counts of fiber and protein products were −1.34 and −1.22 log CFU/g, respectively. However, no aerobic or coliform cells were detected in any other health functional food products (vitamins, minerals, probiotics, milk thistle extract, propolis, eicosapentaenoic acid, docosahexaenoic acid, or lutein products), and no E. coli was detected in any of the categories. These results can potentially be used to update the microbial criteria of the Health Functional Food Code.

  • Indicator organisms were monitored in 14 functional health food categories.

  • Coliform bacteria were detected in powdered red ginseng products.

  • Coliforms were cultivated on nutrient agar; one of them was identified as Pantoea species.

  • For microbe control, HACCP should be implemented properly in manufacturing.

  • Results can be used to update the criteria of coliforms in the Korean Health Functional Food Code.

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