Vaccine effectiveness (VE) was determined with a case-cohort approach using Cox regression. Cases with confirmed systemic Hib infections in children born from 1 August 2000 to 31 December 2004 were ascertained through two independent nationwide active surveillance systems. A representative cohort of 1303 children born in the same time frame was randomly sampled in a nationwide immunisation survey. Thirty cases were eligible for VE calculation; 19 were unvaccinated and 11 vaccinated with hexavalent vaccines. VE was 68.4% (95% CI: 19.0-87.6) for incomplete primary series and 90.4% (95% CI: 70.6-96.8) for the full primary series. For full immunisation VE was 100.0% (95% CI: 52.7-100.0). Hexavalent vaccines show a high effectiveness against invasive Hib disease in Germany.