The design and construction of a miniaturized CE system has been developed for the analysis of clinically important compounds; serotonin and rac-propranolol. Chiral separation of rac-propranolol was investigated by using native and derivatized CDs at varios pH levels (e.g. 2.5, 4.0, 6.0, 9.0). Confocal fluorescence microscopy was used for the native direct detection of target compounds. Analysis time obtained under the optimum separation conditions was 84 s. LOD and LOQ values of serotonin were found as low as 22 and 72.6 fg/microL while these limits were 44 and 145.2 fg/microL for popranolol enantiomers, respectively. LOD and LOQ values were found to be the lowest limits reported before. The calibration curves were linear in the concentration range of 40-1500 fg/microL with the determination coefficients between 0.9994 (+/-0.01) and 0.9997 (+/-0.02).