The Eurocat registry Northern Netherlands (NNL) has been used in regional context, as well as in national/international context, to describe the epidemiology of oral clefts (OC). However, the region NNL seems to have prevalence data different from Dutch national registries and certain other European areas. This may be due to differences in registration methods or geographical variation. To investigate whether the prevalence of OC live births varies regionally in the Netherlands, we established time trends for NNL and the rest of the Netherlands over 1997–2007 using data from two national registries (the OC Registry and The Netherlands Perinatal Registry) and a regional registry (Eurocat NNL). We found that the overall live-birth prevalence—comprising cleft lip/alveolus ± cleft palate and cleft palate only—was significantly higher in NNL (15.1–21.4 per 10,000) than in the rest of the Netherlands (13.2–16.1 per 10,000). None of the registries showed significant trends for NNL, whereas both national registries showed that the live-birth prevalence of cleft lip/alveolus ± cleft palate decreased significantly in the rest of the Netherlands. Despite some differences in prevalence between the registries, they showed similar regional variation in prevalence and trends. In conclusion, the prevalence of OC live births varies significantly in the Netherlands, not only between but also within registries. This underlines that extrapolation of regional cleft data should be done with caution. To further investigate OC etiology and evaluate preventive strategies, future studies should consider geographical differences—between and within countries—regarding the various cleft sub-phenotypes among live births, stillbirths, and pregnancy terminations. © 2011 Wiley Periodicals, Inc.