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Background. Immunisations are one of the most cost-effective public health interventions available and South Africa (SA) has implemented a comprehensive immunisation schedule. However, there is disagreement about the level of immunisation coverage in the country and few studies document the immunisation coverage in rural areas.Objective. To examine the successful and timely delivery of immunisations to children during the first 2 years of life in a deeply rural part of the Eastern Cape Province of SA.Methods. From January to April 2013, a cohort of sequential births (N=470) in the area surrounding Zithulele Hospital in the OR Tambo District of the Eastern Cape was recruited and followed up at home at 3, 6, 9, 12 and 24 months post birth, up to May 2015. Immunisation coverage was determined using Road-to-Health cards.Results. The percentages of children with all immunisations up to date at the time of interview were: 48.6% at 3 months, 73.3% at 6 months, 83.9% at 9 months, 73.3% at 12 months and 73.2% at 24 months. Incomplete immunisations were attributed to stock-outs (56%), lack of awareness of the immunisation schedule or of missed immunisations by the mother (16%) and lack of clinic attendance by the mother (19%). Of the mothers who had visited the clinic for baby immunisations, 49.8% had to make multiple visits because of stock-outs. Measles coverage (of at least one dose) was 85.2% at 1 year and 96.3% by 2 years, but 20.6% of babies had not received a second measles dose (due at 18 months) by 2 years. Immunisations were often given late, particularly the 14-week immunisations.Conclusions. Immunisation rates in the rural Eastern Cape are well below government targets and indicate inadequate provision of basic primary care. Stock-outs of basic childhood immunisations are common and are, according to mothers, the main reason for their children's immunisations not being up to date. There is still much work to be done to ensure that the basics of disease prevention are being delivered at rural clinics in the Eastern Cape, despite attempts to re-engineer primary healthcare in SA.