Conventional and semi-recessed localized oxidation of silicon (LOGOS) processes have been compared in terms of junction current leakage. Three different Si3N4 etch chemistries, SF6/CHF3-SF6/HBr/O-2, CHF3/CF4/Ar, and CHF3/CF4/Ar/CO, have been used to etch active Si3N4 with two types of plasma etchers, conventional silicon nitride and silicon oxide etchers. It has been found that the junction leakage current with CHF3/CF4/Ar id the semi-recessed LOGOS has slightly higher value than that which the convectional LOGOS. However, with CO addition to CHF3/CF4/Ar gases, the junction leakage current resulted from plasma-induced damage on silicon substrate is much higher. The results obtained from X-ray photoelectron spectroscopy and atomic force microscopy indicate that carbon-rich perfluoronated polymers and plasma etch induced silicon substrate roughness with CHF3/CF4/Ar/CO gases contribute to the higher junction leakage.