Different solvent extracts of Nigella sativa seeds and Saussurea lappa roots were investigated for their antimicrobial activity against some Gram negative bacteria isolated from clinical samples from neonatal intensive care unit (NICU) from King Khalid Hospital, Tabuk, Kingdom of Saudi Arabia.Ten clinical isolates, Pseudomonas aeruginosa (n=5), Serratia marcescens (n=2), Proteus mirabilis (n=2) and Sphingomonas paucimobilis (n=1). These isolates were multidrug resistant. The methanolic extract of S. lappa showed high antimicrobial activity rather than that of Nigella sativa seeds especially against Sphingomonas sp. and Serratia sp.. Both methanolic extracts of  S. lappa roots and Nigella sativa seeds showed antibacterial activity against Pseudomonas sp. and Proteus sp with varying extents. The chemical composition of the investigated two plant extracts was examined. It contained phenols, tannins and flavenoids. The emergence of antibiotic resistance and the high risk of the abuse of antibiotics, highlight the need of using alternative agents that have low risk and costless.