Streptococcus equi ssp zooepidemicus (Sez) is a zoonotic pathogen for people in contact with horses. Human infections associated with Sez are however rare, compared to the common presence of Sez in horses. Here, we compared Sez isolates from severe human infections to those isolated from horses to obtain insight into the epidemiology of Sez. Within half a year in 2011, three unrelated cases (Cases 1 to 3) of severe, disseminated Sez infections occurred in men working with horses in eastern Finland. Nasal swabs from horses related to Case 1 (stable A) and Case 2 (stable B) were collected, and Sez were isolated. The contact stable of Case 3 was not sampled. Altogether 14 Sez isolates were analysed: three from Cases 1 to 3, five from stable A, one from stable B, and five from four other stables in the region. Only three equine isolates were from diseased animals. The isolates were analysed using pulsed field gel electrophoresis with SmaI (SmaI-profile), multi locus sequence type analysis (MLST) and sequencing a part of the SzP protein gene (szP type). The isolate from Case 1 was identical with all methods to an equine isolate from stable A. The isolate from Case 2 was dissimilar to the equine isolate from contact stable B, but the MLST and szP types were identical to those of Case 1. The SmaI-profiles of the strains from Cases 1 and 2 differed by 4 bands. The isolate from Case 3 had the same szP type and an almost identical SmaI-profile as an isolate from an unrelated stable. In conclusion, all Sez isolates from humans were closely related to those from horses. The two human isolates were clonally closely related. The results emphasize that Sez transmitted from horses can lead to severe infectious disease in humans.