Giardia lamblia is a major cause of diarrhoea in children, especially those attending day-care centres (DCCs). Only Giardia assemblages A and B infect humans. Given the lack of assemblage-specific epidemiological data, we aimed to identify risk factors for infection by assemblages A and B in DCC attendees. During 2010-2013, 5,015 faecal samples from ≤4-year-old children attending 40 DCCs participating in laboratory surveillance in the Netherlands were tested for Giardia using RT-PCR. Giardia-positive samples were typed for identification of assemblages A and B. We compared child- and DCC-level characteristics of Giardia-positive children with those of Giardia-negative children using mixed-effects logistic regression. Overall, 226 samples (4.5 %) tested positive for Giardia, and assemblages were determined for 138 of them: 62 (45 %) were assemblage A and 76 (55 %) were B. The only risk factor for assemblage A infection was attending DCCs with indoor sandpits and cats during spring/summer (odds ratio [OR] 13.5; 95% CI 1.8-101.3). For assemblage B, risk factors were attending DCCs with dedicated diaper-changing (OR 3.6; 95% CI 1.7-7.6) and laundry (OR 2.3; 95% CI 1.1-4.9) areas. Preventing sick children from attending day-care and having cloth-towels at the DCC decreased the risk of assemblage B infection (OR 0.0; 95% CI 0.0-0.5 and OR 0.3; 95% CI 0.1-0.6 respectively). Risk factors for assemblages A and B infection in DCC-attending children were different, with assemblage B being mainly related to anthroponotic transmission, and assemblage A being related to zoonotic transmission. Given these differences, interventions to reduce the burden of childhood giardiasis cannot ignore those assemblage-specific preferred reservoirs and transmission routes.