We examined uptake of primary immunisations in infancy and the reasons given by mothers for either incompletely or not immunising their infants. We used data from the Millennium Cohort Study, a cohort of 18,819 infants born between September 2000 and January 2002 in the UK. 95.6% infants were reported to be fully immunised, 3.3% partially immunised and 1.1% unimmunised. Mothers most frequently cited medical reasons (45%) for partial immunisation (n=697), but beliefs or attitudes (47%) for no immunisation (n=228). An understanding of maternal reasons for incomplete immunisation status may assist in identifying appropriate interventions to maximise uptake.