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Flooding and heavy rainfall have been associated with waterborne infectious disease outbreaks, however, it is unclear to which extent they pose a risk for public health. Here, risks of infection from exposure to urban floodwater were assessed using quantitative microbial risk assessment (QMRA). To that aim, urban floodwaters were sampled in the Netherlands during 23 events in 2011 and 2012. The water contained Campylobacter jejuni (prevalence 61%, range 14-10(3) MPN/l), Giardia spp. (35%, 0.1-142 cysts/l), Cryptosporidium (30%, 0.1-9.8 oocysts/l), noroviruses (29%, 10(2)-10(4) pdu/l) and enteroviruses (35%, 10(3)-10(4) pdu/l). Exposure data collected by questionnaire, revealed that children swallowed 1.7 ml (mean, 95% Confidence Interval 0-4.6 ml) per exposure event and adults swallowed 0.016 ml (mean, 95% CI 0-0.068 ml) due to hand-mouth contact. The mean risk of infection per event for children, who were exposed to floodwater originating from combined sewers, storm sewers and rainfall generated surface runoff was 33%, 23% and 3.5%, respectively, and for adults it was 3.9%, 0.58% and 0.039%. The annual risk of infection was calculated to compare flooding from different urban drainage systems. An exposure frequency of once every 10 years to flooding originating from combined sewers resulted in an annual risk of infection of 8%, which was equal to the risk of infection of flooding originating from rainfall generated surface runoff 2.3 times per year. However, these annual infection risks will increase with a higher frequency of urban flooding due to heavy rainfall as foreseen in climate change projections.