The modified intra-cerebral challenge assay for acellular pertussis vaccines is used in Japan, Korea, China and possibly other Asian countries as the potency assay for routine release of acellular pertussis (aP) and combination vaccines. National reference standards, typically of whole cell pertussis (Pw) vaccine, are in use in these countries, but there is no agreed international reference standard for acellular pertussis vaccines. We report here the results of a collaborative study initiated in September 2006 in which fourteen laboratories performing the modified intra-cerebral challenge assay took part. These laboratories compared their various national references of Pw vaccine, the third International Standard for whole cell pertussis vaccine, a previously studied two-component freeze-dried aP vaccine preparation coded JNIH-3, and four different aP vaccines in combination with diphtheria and tetanus toxoids. The results of this study show that the modified intra-cerebral challenge assay works reliably although there are inter-laboratory variations in potency estimates. Pw and aP vaccines show apparent differences in dose-response lines in some assay systems. This indicates dissimilarity in performance in at least some of these assay systems. Estimates of relative potency for aP vaccines in terms of the Pw vaccine national or in-house reference preparations differ significantly from one another. Different mouse strains were used in each country and the different strains may also differ in their responsiveness to Pw and aP vaccines. Estimates for different types of aP vaccine formulations show less inter-laboratory variation in terms of JNIH-3 than in terms of the third IS for Pw vaccine and the remaining variation is not apparently related to the different mouse strains. This study thus suggests that an aP vaccine standard would improve inter-laboratory agreement. These data do not show significant dissimilarity in dose-response lines between JNIH-3 and the various vaccine products included, irrespective of the differences in aP components. Available data indicate that JNIH-3 is sufficiently stable to serve as an International Standard. On the basis of these results and with the agreement of the participants, it was proposed that JNIH-3 should be established as an International Standard for acellular pertussis vaccine for use in the modified intra-cerebral challenge assay and other protective bioassays, with an assigned activity of 34 International Units (IU) per ampoule. A WHO Working Group on Standardization of Acellular Pertussis Vaccines: potency assay met in Beijing, China, 7-9 November 2007. This group considered the report of this study, the comments of the participants and implications of the use of JNIH-3 as a reference standard and recommended establishment of JNIH-3 as an International Standard. The results of this study and the report of the Working Group were submitted to the Expert Committee on Biological Standardization (ECBS) of WHO which established JNIH-3 as the first International Standard for acellular pertussis vaccine in the modified intra-cerebral challenge assay and other protective bioassays with an assignment of 34IU per ampoule in October 2008.