Understanding uncertainty is essential for utilizing atmospheric VOC measurements in robust ways to develop atmospheric science. This study describes an inter-comparison of the VOC data, and the derived uncertainty estimates, measured with three independent techniques (PTR-MS, AT-GC-FID and DNPH-HPLC) during the Sydney Particle Study campaigns in 2012. The compounds and compound classes compared, based on objective selection criteria from the available data, were: benzene, toluene, C 8 aromatics, isoprene, formaldehyde, acetaldehyde and acetone. Bottom-up uncertainty analyses were undertaken for each compound and each measurement system. Top-down uncertainties were quantified via the inter-comparisons. Four metrics were used for the inter-comparisons: the slope and intercept as determined by reduced major axis regression, the correlation, and the root mean standard deviation of the observation from the regression line. In all seven comparisons the correlations between independent measurement techniques were high with R 2 values of median 0.93 (range: 0.72–0.98) and small root mean standard deviations of the observations from the regression line with a median of 0.13 (range: 0.04–0.23 ppb). These results give a high degree of confidence that for each comparison the response of the two independent techniques are dominated by the same constituents. The slope and intercept as determined by reduced major axis regression gives a different story. The slopes varied considerably with a median of 1.23 and range 1.08 to 2.03. The intercepts varied with a median of 0.02 and range −0.07 to 0.31 ppb. An ideal comparison would give a slope of 1.00 and an intercept of zero. This analysis identified some poorly understood and poorly quantified sources of uncertainty in the measurement techniques including: the contributions of non-target compounds to the measurement of the target compound for benzene, toluene and isoprene by PTR-MS; and, the under-reporting of formaldehyde, acetaldehyde and acetone by the DNPH technique. As well as these, this study has identified a specific interference of liquid water with acetone measurements by the DNPH technique. These relationships reported for Sydney 2012 were incorporated into a larger analysis with 61 other published inter-comparison studies for the same compounds. Overall for the light aromatics, isoprene and the C 1 –C 3 carbonyls the uncertainty in a set of measurements varies by a factor of between 1.5 and two. These uncertainties (~50 %) are significantly higher than uncertainties estimated using standard propagation of error methods, which in this case were ~22 % or less, and are the result of the presence of poorly understood or neglected processes that affect the measurement and its uncertainty. The uncertainties in VOC measurements identified here should be considered when: assessing the reliability of VOC measurements from individual instruments; when utilising VOC data to constrain and inform air quality and climate models; when using VOC observations for human exposure studies; and, when comparing ambient VOC data with satellite retrievals.