A comparison between ultrasonication and microwave irradiation as tools to achieve a rapid sample treatment for the analysis of banned doping substances in human urine by means of gas chromatography-mass spectrometry (GC-MS) was performed. The following variables were studied and optimised: (i) time of treatment, (ii) temperature, (iii) microwave power and (iv) ultrasonic amplitude. The results were evaluated and compared with those achieved by the routine method used in the World Anti-Doping Agency (WADA) accredited Antidoping Laboratory of Rome. Only under the effect of the ultrasonic field was it possible to enhance the enzymatic hydrolysis reaction rate of conjugated compounds. Similar reaction yield to the routine method was achieved after 10 min for most compounds. Under microwave irradiation, denaturation of the enzyme occurs for high microwave power. The use of both ultrasonic or microwave energy to improve the reaction rate of the derivatisation of the target compounds with trimethyliodosilane/methyl-N-trimethylsilyltrifluoroacetamide (TMSI/MSTFA/NH(4)I/2-mercaptoethanol) was also evaluated. To test the use of the two systems in the acceleration of the reaction with TMSI, a pool of 55 banned substances and/or their metabolites were used. After 3 min of ultrasonication, 34 of the 55 compounds had recoveries similar to those obtained with the classic procedure that lasts for 30 min (Student's t test, n = 5), 18 increased to higher silylation yields, and for the compounds 13 beta,17 alpha-diethyl-3 alpha,17 beta-dihydroxy-5 alpha-gonane (norboletone metabolite 1), metoprolol and metipranolol the same results were obtained increasing the ultrasonication time to 5 min. Similar results were obtained after 3 min of microwave irradiation at 1,200 W. In this case, 30 of the 55 compounds had recoveries similar to the classic procedure (Student's t test, n = 5) whilst 18 had higher silylation yields. For the compounds 3 alpha-hydroxy-1 alpha-methyl-5 alpha-androstan-17-one (mesterolone metabolite 1), 17 alpha-ethyl-5 beta-estrane-3 alpha,17 beta,21-triol (norethandrolone metabolite 1), epioxandrolone, 4-chloro-6 beta,17 beta-dihydroxy-17 alpha-methyl-1,4-androstadien-3-one (chlormetandienone metabolite 1), carphedon, esmolol and bambuterol the same results were obtained after 5 min under microwave irradiation.