Background Perinatal mortality is an important indicator of health. European comparisons of perinatal mortality show an unfavourable position for the Netherlands. Our objective was to study regional variation in perinatal mortality within the Netherlands and to identify possible explanatory factors for the found differences. Methods Our study population comprised of all singleton births (904,003) derived from the Netherlands Perinatal Registry for the period 2000–2004. Perinatal mortality including stillbirth from 22+0 weeks gestation and early neonatal death (0–6 days) was our main outcome measure. Differences in perinatal mortality were calculated between 4 distinct geographical regions North-East-South-West. We tried to explain regional differences by adjustment for the demographic factors maternal age, parity and ethnicity and by socio-economic status and urbanisation degree using logistic modelling. In addition, regional differences in mode of delivery and risk selection were analysed as health care factors. Finally, perinatal mortality was analysed among five distinct clinical risk groups based on the mediating risk factors gestational age and congenital anomalies. Results Overall perinatal mortality was 10.1 per 1,000 total births over the period 2000–2004. Perinatal mortality was elevated in the northern region (11.2 per 1,000 total births). Perinatal mortality in the eastern, western and southern region was 10.2, 10.1 and 9.6 per 1,000 total births respectively. Adjustment for demographic factors increased the perinatal mortality risk in the northern region (odds ratio 1.20, 95% CI 1.12–1.28, compared to reference western region), subsequent adjustment for socio-economic status and urbanisation explained a small part of the elevated risk (odds ratio 1.11, 95% CI 1.03–1.20). Risk group analysis showed that regional differences were absent among very preterm births (22+0 – 25+6 weeks gestation) and most prominent among births from 32+0 gestation weeks onwards and among children with severe congenital anomalies. Among term births (≥ 37+0 weeks) regional mortality differences were largest for births in women transferred from low to high risk during delivery. Conclusion Regional differences in perinatal mortality exist in the Netherlands. These differences could not be explained by demographic or socio-economic factors, however clinical risk group analysis showed indications for a role of health care factors.