Obesity and anaemia remain global public health problems, holding major consequences for human health. The objective was to determine body composition, prevalence of anaemia and iron deficiency, contraception use and associations between variables in rural women in the Free State, South Africa. Design: A cross-sectional study design was applied. Setting: The study was undertaken in rural Trompsburg, Philippolis and Springfontein. Subjects: A total of 134 HIV-uninfected non-pregnant females, aged between 25 and 49 years participated. Exposure and outcome measures: Data were collected on anthropometry, contraception use and biochemical markers of anaemia, iron deficiency and inflammation. Results: Median body mass index (BMI) (28.7 [24.2, 34.7] kg/m 2), waist circumference (90.8 [80.9, 103.0] cm) and body fat percentage (38.8 [34.3, 42.1] %) were classified as unhealthy. Only 2/134 had iron deficiency and 1/134 iron deficiency anaemia. Overall, 3.8% had low red cell folate levels. Almost half (45.0%) had elevated C-reactive protein (CRP) levels. More than half (54.1%) reported that they regularly menstruate and 71.6% currently or had previously used injectable contraceptives. Mean corpuscular volume (MCV), mean corpuscular haemoglobin (MCH) and transferrin saturation were significantly associated with BMI, waist circumference and body fat percentage. Conclusion: A predominant pattern of malnutrition, characterised by overweight and obesity, was prevalent. Risk for iron deficiency was associated with obesity. Prevalence of iron deficiency could be underestimated due to the large percentage with elevated CRP levels. Interventions should aim to improve the nutritional status of these women in order to reduce their risk for both chronic diseases and anaemia.