The objective of this study was to analyze overall contents of biogenic amines in Miso and thereby evaluate the safety of the food. Through HPLC analysis of 22 different Miso products, it was found that most samples had low biogenic amine contents. However, some samples contained both histamine and tyramine close to hazardous levels of the amines, which indicate that the amounts of biogenic amines in Miso are not completely within the safe level for human health. Meanwhile, the biogenic amine contents showed no clear relationship with physicochemical parameters, whereas they revealed a good relationship with the ratio of soybean to other grains used in raw material. Thus, it turned out that biogenic amine contents in Miso are primarily affected by the ratio of raw ingredients, especially soybeans. The aerobic plate counts of Miso samples ranged from 3 to 8 Log CFU/g, and all the strains isolated from Miso samples were found to produce biogenic amines. Most strains were identified to be Bacillus subtilis, often regarded as the predominant contaminant bacteria in Miso, and highly capable of producing tyramine and spermine. Taken together, therefore, this study suggests that variability of biogenic amine contents in Miso are primarily attributed to the ratio of raw ingredients in the food that affects the relative contribution level of bacterial contaminants to the contents.