The type of infant feeding at hospital discharge was compared in Baby-Friendly (BF), non-BF hospitals, neonatal intermediate care units (NICU), and perinatal centres (PC) in the Czech Republic. Data from 660 355 infants born from 2000 to 2006 was collected retrospectively from newborn reports. The exclusive breastfeeding rates decreased in BF hospitals from 92.9% in 2000 to 90.3% in 2006, whereas in non-BF hospitals from 89.4% in 2000 to 87.6% in 2006. Partial breastfeeding in BF hospitals increased from 3.6% in 2000 to 5.7% in 2006, whereas in non-BF hospitals from 4.9% in 2000 to 6.8% in 2006. Exclusive formula feeding rates changed only slightly. The risk of not being exclusively breastfed was higher in non-BF than in BF hospitals (unadjusted OR = 1.57, 95% CI 1.47-1, 68 for year 2000, OR = 1.6, 95% CI 1.53-1.68 for year 2004, and OR = 1.36, 95% CI 1.3-1.42 for year 2006). In hospitals with PC and NICU the exclusive breastfeeding rates were lower than in hospitals without those departments.