Insight in the molecular structure of humic acid (HA) and fulvic acid (FA) can contribute to identify relationships between their molecular properties, and further our quantitative abilities to model important organic matter functions such as metal complexation and association with mineral surfaces. Pyrolysis gas chromatography/mass spectrometry (Py-GC-MS) is used to compare the molecular composition of HA and FA. A systematic comparison was obtained by using samples from different environmental sources, including solid and aqueous samples from both natural and waste sources. The chemical signature of the pyrolysates was highly variable and no significant difference between HA and FA was found for major chemical groups, that is, carbohydrates, phenols, benzenes, and lignin phenols, together accounting for 62-96% of all quantified pyrolysis products. However, factor analysis showed that within each sample, FAs consistently differed from corresponding HAs in a larger contribution from mono- and polyaromatic hydrocarbons and heterocyclic hydrocarbons, together accounting for 3.9-44.5% of the quantified pyrolysis products. This consistent difference between FAs and corresponding HAs, suggests that their binding properties may, in addition to the carboxyl and phenolic groups, be influenced by the molecular architecture. Py-GC-MS may thus contribute to identify relationships between HA and FA binding- and molecular-properties.