Of the total of 35 clinical isolates from blood and/or cerebrospinal fluid in patients from the Zagreb area in the period from 1996-1999 Neisseria meningitidis serogroup B was identified in 33 (94%). N. meningitidis strains with decreased susceptibility to penicillin have been occurring in Zagreb since 1998, and during the two-year period in this study we isolated 3/19 (16%) such strains (MIC, 0.12 microgram/ml). Molecular typization of strains with decreased susceptibility to penicillin shows that they do not belong to a particular meningococcal clonal group. All isolated N. meningitidis strains were susceptible to the third generation cephalosphorins, quinolones and chloramphenicol. A single strain (3%) was resistant to rifampin, but 13/35 (37%) were resistant to trimethoprim/sulfamethoxazole. Consequently, trimethoprim/sulfamethoxazole is not recommended for chemoprophylaxis of meningococcal disease. Initially patients with meningococcal disease should be treated with the third generation cephalosporins, and further treatment should be continued in accordance with the antimicrobial susceptibility testing results. This study emphasizes the utility and importance of meningococcal disease monitoring throughout the Republic of Croatia.