In 2012, cryptosporidiosis cases increased in the Netherlands, but no single source was identified. In April 2013, we began a three year population based case-control study, coupled with genotyping, to identify risk factors for sporadic cryptosporidiosis. Cryptosporidium cases were laboratory confirmed (microscopy or PCR), followed by C. hominis and C. parvum species determination testing. We analysed data by study year, combined and by species. We performed single variable analysis and variables with a P-value ≤0.10 were included in a multivariable logistic regression model adjusting for age, sex and season. The study included 609 cases and 1,548 frequency-matched controls. C. parvum was the predominant species in the first two study years, shifting to C. hominis in the third year. Household person-to-person transmission and eating barbequed food were strongly associated with being a case. Eating tomatoes was negatively associated. By study year, person-to-person transmission was an independent risk factor. Analysis by species identified different risk factors for C. parvum and C. hominis cases. This was the first case-control study examining risk factors for sporadic cryptosporidiosis in the Netherlands. Providing information about Cryptosporidium exposure during outdoor activities and improvements in hygiene within households could prevent future sporadic infections.