Savannas are spatially heterogeneous, open ecosystems, thus efforts to quantify canopy structure with methods developed for homogeneous, closed canopies are prone to failure. We examine the applicability of two direct (litterfall, allometry) and five indirect (LAI-2000, TRAC, digital hemispheric photography, digital cover photography, traversing radiometer system) methods to determine leaf area index across a 9 ha domain in an oak-savanna ecosystem in California, USA. Interpretation of the leaf area index measurements is supported by two gap-fraction models. We recommend that leaf inclination angle distribution should be characterized first. For this purpose, we propose a simple, reliable and reproducible method using a digital camera. We show that the combination of digital cover photography and LAI-2000 could provide spatially representative leaf area index, gap fraction and element clumping index. Based on these two indirect methods, we quantify spatially representative element clumping index and leaf area index at ecosystem scale as 0.49 ± 0.10 (mean ± 95% confidence interval) and 0.77 ± 0.27, respectively. In contrast to previous studies in northern ecosystems, measurement and modeling results suggest that element clumping index decreases with view zenith angle, most likely due to apparent changes of tree distribution pattern with the view zenith angle. Our results highlight the importance of ecosystem-scale clumping effects for the adequate quantification of tree leaf area index in savannas. Finally, we suggest a protocol to quantify leaf area index and its associated canopy structure variables in open canopy ecosystems.