OBJECTIVES: We investigated concordance between haemoglobin A1c (HbA1c)-defined diabetes and fasting plasma glucose (FPG)-defined diabetes in a black South African population with a high prevalence of obesity. DESIGN: Cross-sectional study. SETTING: Rural South African population-based cohort. PARTICIPANTS: 765 black individuals aged 40-70 years and with no history of diabetes. PRIMARY AND SECONDARY OUTCOME MEASURES: The primary outcome measure was concordance between HbA1c-defined diabetes and FPG-defined diabetes. Secondary outcome measures were differences in anthropometric characteristics, fat distribution and insulin resistance (measured using Homoeostatic Model Assessment of Insulin Resistance (HOMA-IR)) between those with concordant and discordant HbA1c/FPG classifications and predictors of HbA1c variance. RESULTS: The prevalence of HbA1c-defined diabetes was four times the prevalence of FPG-defined diabetes (17.5% vs 4.2%). Classification was discordant in 15.7% of participants, with 111 individuals (14.5%) having HbA1c-only diabetes (kappa 0.23; 95% CI 0.14 to 0.31). Median body mass index, waist and hip circumference, waist-to-hip ratio, subcutaneous adipose tissue and HOMA-IR in participants with HbA1c-only diabetes were similar to those in participants who were normoglycaemic by both biomarkers and significantly lower than in participants with diabetes by both biomarkers (p<0.05). HOMA-IR and fat distribution explained additional HbA1c variance beyond glucose and age only in women. CONCLUSIONS: Concordance was poor between HbA1c and FPG in diagnosis of diabetes in black South Africans, and participants with HbA1c-only diabetes phenotypically resembled normoglycaemic participants. Further work is necessary to determine which of these parameters better predicts diabetes-related morbidities in this population and whether a population-specific HbA1c threshold is necessary.