This work assesses the main sources of uncertainty of the determination of several secondary organic aerosol (SOA) components. The evaluation of the uncertainty associated with analytical methods is essential in order to demonstrate that the results obtained in routine analysis are reliable. The current work has thoroughly evaluated the sources of uncertainties associated with the analytical method employed to quantify the SOA produced from photo-oxidation of complex mixtures of volatile organic compounds (VOCs) in smog chambers. Measurement uncertainties were calculated by applying a bottom-up approach. The combined uncertainty of the analytical method ranged from 8% for glyoxal to 29% for methyl benzoquinone. The results clearly show that the determination of some SOA compounds is associated with a high level of uncertainty, and thus the quantification process for these at lower levels remains challenging.