BackgroundDiphtheria is a severe respiratory or cutaneous infectious disease, caused by exotoxin producingCorynebacterium diphtheriae,C. ulceransandC. pseudotuberculosis. Diphtheria is once again prevalent due to breakdown of immunisation programmes, social disruption and unrest.AimThis study describes the notified diphtheria cases in the Netherlands between 2000–2021 and isolates that were sent to the National Institute for Public Health and the Environment (RIVM).MethodsFile investigation was performed including all notified cases and isolates ofC. diphtheriae,C. ulceransandC. pseudotuberculosisthat were tested for toxin production using a toxin-PCR and Elek test. An exploratory review was performed to understand transmission in populations with a high vaccination uptake.ResultsEighteen diphtheria notifications were made with confirmed toxigenicC. diphtheriae(n= 9) orulcerans(n= 9) between 2000 and 2021. Seventeen (94.4%) presented with a cutaneous infection. All cases with a suspected source abroad (n= 8) concerned infection withC. diphtheriae. In contrast, 9/10 cases infected in the Netherlands were caused byC. ulcerans, a zoonosis. Secondary transmission was not reported. Isolates ofC. ulceranssent to the RIVM produced more often the diphtheria exotoxin (11/31; 35%) thanC. diphtheriae(7/89; 7.9%).ConclusionBoth human-to-human transmission ofC. diphtheriaeand animal-to-human transmission ofC. ulceransrarely occurs in the Netherlands. Cases mainly present with a cutaneous infection. Travel-related cases remain a risk for transmission to populations with low vaccination coverage, highlighting the importance of immunization and diphtheria control measures.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12879-023-08388-5.