This work presents the development of an analytical method based on capillary electrophoresis with diode array detection for the analysis of drugs of abuse and biotransformation products in vitreous humor. Composition of the background electrolyte, implementation of an online pre-concentration strategy and sample preparation procedures were objects of study. The complete electrophoretic separation of 12 analytes (amphetamine, methamphetamine, 3,4-methylenedioxyamphetamine (MDA), 3,4-methylenedioxymethamphetamine (MDMA), 3,4-methylenedioxyethylamphetamine (MDEA), ketamine, cocaine, cocaethylene, lidocaine, morphine, 6-monoacetylmorphine and heroin) and the internal standard N-methyl-1-(3,4-methylenedioxyphenyl)-2-butamine (MBDB) was obtained within 13 min of run. The method was validated presenting good linearity (r2 > 0.99), recovery ≥90%, precision better than 12% RSD and acceptable accuracy in the range of 86–118% at three concentration levels (50, 100 and 500 ng/mL). LODs and LOQs in the order of 1–5 ng/mL and 5–10 ng/mL, respectively, were obtained. After validation, the method was applied to eighty-seven vitreous humor samples and the results were compared to those obtained by a liquid chromatography tandem mass spectrometry (LC-MS/MS) screening method, routinely used by the forensic toxicology laboratory of the Sao Paulo State Police, Brazil. Cocaine was detected in 7.1%, cocaethylene in 3.6%, lidocaine in 2.4% and ketamine in 1.2% of the total number of analyzed samples.