Most human hantavirus infections in Denmark have been registered on the Fyn island with Puumala hantavirus hosted by Clethrionomys glareolus as the causative agent. To search for other known European hantaviruses in Denmark, we analyzed 101 Apodemus spp. mice trapped on the Lolland island. Genome sequences of Saaremaa hantavirus (SAAV) were recovered from one of the A. agrarius, thus suggesting SAAV presence in Denmark. We also analyzed serum samples from a patient from Lolland with a history of hantavirus-like infection, probably caused by SAAV. Thus, in addition to Puumala virus, SAAV can impose a threat for the human health in Denmark.