One-year prospective study for surveillance of the resistance of invasive bacteria in accordance with the EARSS (European Antimicrobial Resistance Surveillance System) Protocols was performed in Estonia in 2004. The ratio of Gram-positive to Gram-negative pathogens was 1.9. For estimation of CONS (coagulase-negative staphylococci) prevalence and for standardisation of their resistance surveillance, generally accepted algorithms for exclusion of contaminants are needed. Overall antimicrobial resistance among major bloodstream pathogens was relatively low and Gram-positive indicator pathogens remained quite susceptible in Estonia. E. coli and Klebsiella spp. were sensitive to the tested agents, while the susceptibility pattern of A. baumannii and P. aeruginosa varied significantly. The inclusion of invasive Gram-negative pathogens in antimicrobial resistance surveillance is relatively inexpensive owing to the low number of strains occurring in our country. However, this gives useful information of the local pathogen profile and susceptibility for detection of emerging resistance trends as well as for empirical treatments of suspected infections.