The feasibility of freeze-dried urine samples containing doping agents to be used in intercomparison exercises and/or as reference materials has been evaluated. Freeze-dried urine samples containing caffeine, ephedrine derivatives (ephedrine, methylephedrine, norephedrine, pseudoephedrine and norpseudoephedrine), amphetamine derivatives (amphetamine, metamphetamine, 3,4-methylenedioxyamphetamine and 3,4-methylenedioxymethamphetamine) and testosterone and epitestosterone glucuronides have been evaluated. For preparation of the samples, blank urines previously subjected to filtration for clarification were fortified with standard solutions of the corresponding compounds and filtered under sterile conditions. Some aliquots of the sterile liquid samples were used for homogeneity testing, others were stored at −80 °C for reference purposes, and the rest were subjected to lyophilisation. Freeze-dried urine samples were stored at 4–8 °C and their stability was assessed for a period up to 18 months. Results obtained showed minimal differences (lower than 5%) between lyophilised and non-lyophilised aliquots (stored at −80 °C) at all time periods except for amphetamine (up to 18%) and norpseudoephedrine (up to 10%). Nevertheless, such differences remained constant over the entire period of study, indicating that the loss of analytes was due to the initial lyophilisation process. The loss of analytes in freeze-dried samples was due to their volatility. Furthermore, an increase in pH by 1 unit was observed following reconstitution of samples prepared from drug-free urine of commercial origin.