Objectives To assess childhood vaccination coverage at first, second and fifth birthdays by ethnicity in London between 2006/2007 and 2010/2011 and identify factors relating to lower coverage.

Design Data concerning receipt of diphtheria-containing vaccines were extracted from child health information systems (CHISs) and sent to the Health Protection Agency.

Setting Nine London Primary Care Trusts (PCTs).

Participants Records for 315 381 children born April 2001–March 2010.

Main outcome measures Receipt of a full primary course of diphtheria-containing vaccines at first and second birthdays, and a primary course and preschool booster at fifth birthday.

Results Consistently good vaccine coverage of the primary course (>88% at first birthday, >89% at second birthday) was achieved across the five largest ethnic groups. Coverage of the preschool booster at fifth birthday was >65% across the five largest ethnic groups. Lowest coverage was observed in smaller ethnic groups. Deprivation was not a strong indicator of coverage overall, and for most ethnic groups there was no relationship between deprivation and coverage. Coverage was significantly lower in children not assigned to a general practitioner practice in the CHIS.

Conclusions Smaller, less well-established ethnic groups within a PCT may require specific targeting to ensure children are fully immunised and to improve record keeping. Unregistered children need particular attention and may be missed by current scheduling processes in London. In order to monitor the impact of the current National Health Service (NHS) reorganisation on inequalities in access to healthcare data on country of birth, in addition to ethnicity, should be available for analysis.