There are some concerns because there have been a number of cases of food poisoning. Washing and sanitizing your sprouter, your hands, and using clean filtered water and organic seed will minimize the risks however. Unless you have a compromised immune system (AIDS, chemotherapy, old age) I wouldn’t worry about it. Part of an article about sprout safety is pasted below:
Sprouts and Foodborne Disease
Food Safety & Hygiene ~ A bulletin for the Australian Food Industry
Food Science Australia
November 2000
The consumption of raw sprouted seeds has led to a large number of outbreaks of foodborne illness in a great number of countries. Alfalfa sprouts have been implicated most often, but other sprouts have also caused illness. Contaminated seed was the likely source of the pathogens in these outbreaks. While there have been no reported outbreaks from sprouts produced in Australia, seeds grown in Australia have been associated with outbreaks in other countries.
The first recorded outbreak of foodborne disease from the consumption of raw, sprouted seeds was in 1973 and this was from soy, mustard and cress grown in home-sprouting packs which were contaminated with Bacillus cereus. In 1988, there were large outbreaks of food poisoning in both the UK and Sweden from eating raw mung bean sprouts. Five different Salmonella serotypes were associated with the outbreaks, and 3 of these serotypes were detected in bags of mung bean seeds which had come from Australia.
In the following year, sprouts of cress contaminated with S. Gold-Coast were implicated in another outbreak in the UK. In the early 1990s, three outbreaks of salmonellosis from sprouts were identified in Finland. One outbreak of over 490 cases, in both Finland and Sweden, was due to S. Bovismorbificans in alfalfa sprouts and these seeds also had been imported from Australia. Several other outbreaks were reported in the 1990s in which salmonellae were implicated and alfalfa sprouts were the usual vehicle.
White radish sprouts used in school lunch programs were associated with a very large outbreak of Escherichia coli O157:H7 infections with more than 6000 cases in Japan in 1996. In the next year also, smaller outbreaks occurred in two Japanese cities from radish sprouts contaminated with E. coli O157:H7. Two outbreaks of E. coli O157 infection have also occurred in the US which have been linked to the consumption of alfalfa sprouts or an alfalfa/clover mixture. E. coli O157 is one member of a group of pathogenic E. coli known as enterohaemorrhagic E. coli or EHEC, for short.
Bacterial growth during sprouting
In the production of sprouts, seeds are soaked in water for a few hours and then held at 20–26°C for some days while being intermittently sprayed with water during germination and growth. These conditions, together with nutrients from the seeds and sprouts, provide good conditions for bacterial growth. The population of bacteria naturally on the seed increases rapidly. During the pre-germination soaking, the population may increase 10-fold or more. After two days of germination, even under hygienic conditions, bacterial numbers on sprouts will be up to millions per gram. The population frequently contains very large numbers of coliforms as well as many thermotolerant coliforms (ie able to grow at 44°C) that are normally associated with plant material. These may mistakenly be regarded as “faecal coliforms”. Some (eg Klebsiella oxytoca and Enterobacter cloacae) also produce indole and may be mistaken for E. coli.
If a pathogen is present on the seeds, it too may grow extensively during germination. In the B. cereus outbreak in the 1970s, cells of B. cereus grew from about 100 per gram on the seeds to over a million per gram on the sprouts. Proliferation of Salmonella, E. coli O157 and Listeria monocytogenes has also been demonstrated to occur during germination and growth of sprouts. It is the considerable growth of bacteria during the normal process of sprouting that increases the risk of foodborne disease from sprouts compared to that from other vegetables.
Contamination of sprouts
While contamination with pathogens can occur from the water used in germination and sprouting or from the equipment used in the sprouting process, seed is the usual source. Seed can be contaminated in the field from agricultural water, from improperly composted manure, contaminated soil, and from feral or grazing farm animals. Seed can be contaminated from harvesting equipment, from residues in storage containers and screw-conveyors. Seed can be contaminated at the seed-mill where it is cleaned, graded and packed. Salmonellae have frequently been found in the dust that accumulates during seed cleaning. Good agricultural and handling practices will reduce seed contamination. However, total prevention of contamination is not possible.
http://www.sproutnet.com/Reports/sprouts_and_foodborne_disease.htm