Multiresistant Streptococcus pneumoniae infections are of great concern as treatment failures may occur with commonly used treatment regimens using β-lactams and macrolides. The proportion of non-susceptible S. pneumoniae differs from country to country. In Denmark, the proportion of invasive penicillin- or erythromycin-non-susceptible isolates is still low. The aim of this study was to characterise and compare invasive and non-invasive penicillin-non-susceptible and erythromycin-resistant pneumococcal isolates from the same geographic area and the same time period with respect to serotype and antibiotic susceptibility profile. We aimed to identify which serotypes were multiresistant among Danish isolates and to confirm or reject whether there was a difference in serotype distribution and resistance profiles between invasive and non-invasive isolates. We observed that non-invasive penicillin-non-susceptible pneumococci had higher serotype diversity than invasive isolates. This was not the case for erythromycin-resistant pneumococci. The dominant serotypes among non-susceptible invasive isolates were serotypes 9V and 14, whereas the dominant serotypes among non-susceptible non-invasive isolates were serotypes 19F, 14, 9V, 6B and non-typeable (NT). Non-invasive isolates were also more likely to be resistant to three or more antimicrobial agents than invasive isolates, however isolates being multiresistant were often co-resistant to the same antimicrobial agents.