The compounds 8-ethyl- (2), 8-butyl- (3), 8-hexyl- (4), 8-octyl- (5), 8-decyl- (6) and 8-dodecylberberine chloride (7) were synthesized and tested for their antimicrobial activity in vitro to evaluate structure-activity relationships. Substitution of the alkyl groups at C-8 led to significant changes in the antimicrobial activity. All compounds were more potent against the tested microorganisms than berberine (1), especially against Gram-positive bacteria. The antimicrobial activity increased as the length of aliphatic chain was elongated and then decreased gradually when the alkyl chain exceeded eight carbon atoms. 8-octylberberine (5) displayed the highest antimicrobial activity of all compounds. The toxicity of compounds 2 - 7 was stronger than that of 1. However, upon elongating the aliphatic chain, the toxicity decreased gradually.