Background The potential for outbreaks due to Enteroviruses (EV) with respiratory tropism, such as EV-D68, and the detection of new and rare EV species C is a concern. These EVs are typically not detected in stool specimens and may therefore be missed by standard EV surveillance systems. Following the North American outbreak of EV-D68 in 2014, Denmark piloted an enhanced EV surveillance system that included the screening of respiratory samples. Objectives We aim to report clinical manifestations and phylogenetic descriptions from the rare and emerging EVs identified thereby demonstrating the usefulness of this system. Study design Positive EV samples received through the enhanced non-polio EV pilot surveillance system were characterized by sequencing fragments of VP1, VP2 and VP4 capsid proteins and clinical observations were compiled. Results Between January 2015 and October 2016, six cases of rare genotypes EV-C104, C105 and C109 and nine cases of EV-D68 were identified. Patients presented with mild to moderately severe respiratory illness; no paralysis occurred. Distinct EV-C104, EV-C109 and EV-D68 sequences argue against a common source of introduction of these genotypes in the Danish population. Conclusions The enhanced EV surveillance system enabled detection and characterization of rare EVs in Denmark. In order to improve our knowledge of and our preparedness against emerging EVs, public health laboratories should consider expanding their EV surveillance system to include respiratory specimens.