Objective The purpose of this cross-sectional study was to assess the prevalence of dental caries in children with cleft lip, alveolus, and/or cleft palate living in central Germany between 1996 and 2010. Participants A total of 295 children 1 to 6 years of age from three birth cohorts (BC) with clefts from central Germany were included in the study. They were compared with 548 1- to 6-year-old cleft-free children from the same region. Setting Children with clefts underwent a dental examination in an outpatient dental clinic at the University of Leipzig. The first BC was examined between 1996 and 1998, the second between 2002 and 2004, and the third between 2008 and 2010. Controls were examined at day-care centers in Leipzig during the same periods. Main Outcome Measure The standard dental caries index for the primary dentition (dmf/t3-4) was used for clinical assessment. Results Over the entire study period, the mean prevalence of dental caries in deciduous teeth was significantly higher (1.32 dmf/t3-4) in children with clefts compared with cleft-free children. However, a decline in caries (approximately 1 dmf/t3-4) and an increase in the proportion of children with healthy primary dentition were observed in both groups. These results represent a caries decline of 61% in children with clefts. Conclusions Caries rates for children 1 to 6 years of age with clefts from central Germany showed a considerable decline over the last years. The caries rates for clefts patients in the third BC (2008 to 2010) was similar to that of cleft-free children in the first BC (1996 to 1998).