The link between carriage and disease is utilized in monitoring effects of vaccines targeting respiratory bacteria. The gold standard for carriage detection is the culturing of live bacteria from nasopharyngeal (pneumococcus) or oropharyngeal (meningococci) swabs. These samples can be complemented with collection of saliva. A critical factor for oral samples is the high density and diversity of bacteria which diminishes the sensitivity of culture. Molecular methods have largely improved the detection of pathogens. By applying molecular diagnostics we have reported oropharyngeal swabs in adults to be superior to nasopharyngeal swabs for the detection of pneumococci. More importantly, we detected a large reservoir of pneumococci in the saliva of carriers, a finding in line with century-old studies reporting on high carriage rates. The use of saliva in the surveillance of pneumococcal disease and of other respiratory diseases needs to be explored