Inequitable access to healthcare has a profound impact on the health of marginalised groups that typically suffer an excess burden of infectious disease morbidity and mortality. The Yanomami are traditionally semi-nomadic people living in widely dispersed communities in Amazonian Venezuela and Brazil. Only communities living in the vicinity of a health post have relatively constant access to healthcare. To monitor the improvement in the development of Yanomami healthcare a cross-sectional survey of 183 individuals was conducted to investigate malaria and anaemia prevalence in communities with constant and intermittent access to healthcare. Demographic and clinical data were collected. Malaria was diagnosed by microscopy and haemoglobin concentration by HemoCue. Prevalence of malaria, anaemia, splenomegaly, fever and diarrhoea were all significantly higher in communities with intermittent access to healthcare (anaemia 80.8% vs. 53.6%, P<0.001; malaria 18.2% vs. 6.0%, P=0.013; splenomegaly 85.4% vs.12.5%, P<0.001; fever 50.5% vs. 28.6%, P=0.003; diarrhoea 30.3% vs.10.7% P=0.001). Haemoglobin level (10.0 g/dl vs. 11.5 g/dl) was significantly associated with access to healthcare when controlling for age, sex, malaria and splenomegaly (P=0.01). These findings indicate a heavy burden of anaemia in both areas and the need for interventions against anaemia and malaria, along with more frequent medical visits to remote areas.