In this paper, a method was described to determine cocaine (COC) and benzoylecgonine (BZE) in human urine samples by GC-MS detection. The extraction of analytes from urine samples was achieved in an Oasis hydrophilic-lipophilic balance column (20 mmx3.9 mm id, dp=25 microm; Waters, USA), incorporated in a multisyringe flow injection system, used for the sample treatment. Finally, to improve the volatility of the BZE, an in-line derivatization reaction with N,O-bis (trimethylsilyl) trifluoroacetamide with 1% trimethylchlorosilane was made microwave-assisted in order to reduce the reaction time. The results showed that the proposed method is a good alternative for the analysis of COC and BZE in urine samples because it offers advantages compared with those described in the literature, which include simplicity in the sample treatment, the sensitivity and selectivity necessary to determine the analytes of interest at low levels in the urine and high sample throughput.