We reviewed laboratory data on non-invasive pneumococcal isolates reported from all diagnostic laboratories in Scotland during the period 1988-99. Of 4491 isolates from hospitalized patients, 654 (64.7%) were from sputum, 79 (7.8%) from the nasopharynx and 278 (27.5%) from other superficial sites. The serogroups included in the 23-valent polysaccharide vaccine caused 96.9% of all non-invasive disease in all age groups. The 7-, 9-, and 11-valent conjugated vaccine serogroups were responsible for 87-94%, 85-93%, 74-81% and 75-84% of non-invasive disease respectively in age groups < 2 years, < or = 5 years, > or = 65 years and all ages. The coverage of non-susceptible penicillin and erythromycin non-invasive isolates was > 99% and > 95% with the 23-valent polysaccharide and 7-11-valent conjugate vaccines respectively. The eight most common serogroups were 23, 9, 6, 19, 14, 3, 15 and 11 (in descending order). The serogroups associated with antimicrobial resistance in non-invasive disease were similar to those found in invasive disease. The finding of a similar serogroup distribution in both invasive and non-invasive disease (regardless of the site of clinical isolate), is consistent with serogroups colonizing non-sterile sites and having the potential to invade. The availability of conjugated vaccines reinforces the importance of systematic surveillance to determine accurately and regularly the coverage of pneumococcal serogroups and types causing both invasive and non-invasive disease.