Current work has evaluated uncertainty associated to quantification of several organic compounds present in particulate matter of atmospheric aerosols, setting out the stages of analytical procedure that contribute most to the global uncertainty. Several sources of uncertainty have been identified, which were clustered into five main contributions: sampling, extraction, clean-up, derivatization and analysis. A discussion of the main contributions to the overall uncertainty is reported, allowing authors to locate the largest ones and plan future improvements. Combined uncertainties ranged between 10-18% (alkanes), 12-16% (PAHs), 10-18% (alcohols) and 9-21% (acids). The analytical procedure was validated by analysing a standard reference material (SRM1649a, urban dust). Also, the proposed method was applied to the analysis of four samples of particulate matter.