This prospective cohort study was performed from April to December 2003 for the purpose of collecting a maximum of 50 non-duplicate isolates of Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae from each of 4 ICUs to determine minimum inhibitory concentrations. The most prevalent species were Enterobacteriaceae (13%), K. pneumoniae and A. baumannii (both 12%). 60% of A. baumannii strains were susceptible to ampicillin/sulbactam and cefepime, 95% to meropenem and imipenem, and 75% to amikacin. 79% of P. aeruginosa strains were piperacillin/tazobactam, 58% ceftazidime, 81% meropenem, 72% imipenem, 69% ciprofloxacin and 97% amikacin susceptible. The susceptibility of K. pneumoniae to meropenem and imipenem was 99%, to ciprofloxacin was 91% and to amikacin was 98%. Gram-negative bacteria (especially K. pneumoniae and A. baumannii) were prevalent in our ICUs compared to other European studies. Carbapenem susceptibility of Estonian strains was higher, but P. aeruginosa sensitivity to ceftazidime was lower, compared to other EU countries.