Developing adequate indicators of biodiversity change is an urgent task for biodiversity studies and policy. An important component of any indicator is a measure of the uncertainty in the estimates it produces. In this paper, we derive the biodiversity intactness variance (BIV) as a formal measure of uncertainty to accompany the recently developed biodiversity intactness index (BII) (Scholes and Biggs [Scholes, R.J., Biggs, R., 2005. A biodiversity intactness index. Nature 434, 45–49]). The BII is based on estimates of baseline species richness, the area of different land-uses, and the abundance of different species under different land uses. The BIV quantifies uncertainty in the abundance estimates, which are the main source of uncertainty in BII. The BII for southern Africa in the year 2000 has been estimated at 84.4%. We calculate the accompanying BIV at 50.4, providing a 95% confidence interval of 76.6–92.2% for BII. By applying the BIV, we can quantify the major sources of uncertainty in the BII for southern Africa: they stem from the abundance estimates for mammals and birds, and for savanna regions and degraded areas. The BIV therefore provides a means for better assessing the state of biodiversity loss and for highlighting research priorities.