The consumption of raw sprouts has increased in popularity worldwide because the food is natural and healthy. However, in Korea, nothing is known on the safety standards of sprout producers or changes in the microbial populations of sprouts during sprouting. We evaluated the microbial safety and quality of sprouts during each step in the sprouting process. Bacteriological analysis showed that seeds had a Total Plate Count (TPC) ranging from 3.04 - 5.21 log CFU/g and coliform counts ranging from 1.80 - 3.86 log CFU/g. TPC and coliform counts increased rapidly during the sprouting process to attain values of 6.99 - 8.26 and 3.70 - 7.15 log CFU/g, respectively, regardless of decontamination of seeds with commercial sanitizer. TPC and coliform counts were on high level after sprouts were washed. Escherichia coli was detected in samples of domestic radish sprouts at all stages from seed to storage, rape sprouts in the stages from soaked seed to storage, and red radish sprouts during sprouting, and no sanitizer was used in any of these processes. Untreated red radish sprouts were also positive for Bacillus cereus at all processing steps and Listeria monocytogenes after germination. However, pathogens were not detected at any sprouting stage of seeds treated with sanitizer. It is necessary to carefully control commercial sprouting, and to develop HACCP guidelines applicable to all sprouting processes, commencing at the first step in raw seed production.