Capillary electrophoresis (CE), high performance thin layer chromatography (HPTLC) and spectrophotometric (SPM) methods were compared for the determination of entacapone in pharmaceutical preparations. And ultrasonication assisted extraction (UAE) coupled with CE determination of cis and trans isomers of entacapone in urine sample was optimized. Resolution of entacapone isomers could not be achieve on RP-HPTLC developed with a native or modified cyclodextrins as a mobile phase additive. Different types aqueous and non-aqueous background electrolytes were tested for the resolution of isomers by CE. Good resolution (Rs similar to 4.9) was achieved on using a non-aqueous background electrolyte (NBGE). Tailing and concentration dependent migration were observed on silica gel HPTLC plates, due to strong adsorption of entacapone. However, the plate developed with tetrahydrofuran (THF), a good baseline separation was achieved. Good recovery of entacapone was achieved in tablet dosage by using non-aqueous extraction solvent system (NAES). All the methods (SPM, HPTLC and CE) the correlation coefficient (R2) were > 0.9993. SPM method is found be simple, convenient and faster than HPTLC and CE for the determination of entacapone in tablet dosage forms. However, the CE method alone found to be useful for separation and determination of cis and trans isomer in tablets and urine samples and it is simple, fast, cost-effective and efficient.