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Pneumococcal disease remains an important cause of invasive and non-invasive disease in Scotland and elsewhere. The Scottish Meningococcus and Pneumococcus Reference Laboratory receives isolates of Streptococcus pneumoniae from diagnostic laboratories around Scotland. Here, the serogroups/types and antibiotic-susceptibility patterns of invasive isolates received between 1999 and 2002 are described. There were a total of 1741 invasive isolates received, the most common serogroups/types being 14 (19.8 %), 9 (10.2 %), 6 (8.3 %), 19 (7.9 %), 23 (7.9 %), 4 (6.5 %), 8 (6.4 %), 3 (5.7 %), 1 (3.8 %), 7 (3.8 %) and 18 (3.4 %). Importantly, serotypes 7 and 8 are not represented in the 7-, 9- and 11-valent pneumococcal conjugate polysaccharide vaccines. There were 67 (3.8 %) isolates considered penicillin non-susceptible, although no penicillin resistance (MIC ⩾ 0.002 mg ml−1) was recorded. One hundred and ninety-four (11.1 %) isolates, predominantly of serotype 14, were resistant to erythromycin, and 12 (0.7 %) were resistant to ciprofloxacin. This information provides an important dataset that will prove essential prior to and during the implementation of pneumococcal conjugate vaccines in the UK.