Methadone has previously been found present in exhaled breath of methadone treated patients. This study aimed at studying if methadone is present in the aerosol fraction of exhaled breath and used different filter sampling techniques for that. Patients receiving methadone maintenance treatment were recruited for the study. Methadone was extracted from filters collecting methadone from exhaled breath using 2-propanol, methanol and ethyl acetate and measured using liquid-chromatography–tandem mass-spectrometry. The limit of quantification was 5 pg/sample and the intra-day imprecision and accuracy within 15%. The recovery of extracting methadone from filters was >90%. Two types of micro-particle filters were used in this study and were compared with the C18 silica filter (Empore) used before. The Glass fiber filter collected methadone from exhaled breath of methadone patients. The amount collected significantly exceeded the amount using the C18 Empore filter (3.6–14-fold), but the variability of amount trapped was large. The second filter type was a polymer filter. Also this filter was able to trap methadone from exhaled breath of methadone patients. The amount and variability was similar to the C18 Empore filter but smaller than the Glass fiber filter. The mean rate of methadone excretion measured with the best polymer filter was 92 pg/min with a range between 20 and 287 (n = 5). The polymer filter has the practical advantage of having a low flow resistance making it possible to sample without pumping assistance. The polymer filter was found to collect >90% of the exhaled methadone. The conclusion of this study was that methadone in exhaled breath is carried in the aerosol fraction known to be formed in the lung as a result of normal breathing.