Schmallenberg virus is an orthobunyavirus that infects ruminants and can cause transient fever, diarrhea, reduced milk production, congenital malformations, and abortions. Following the first suspected cases in Azerbaijan, a surveillance study was launched to determine and follow the situation. Serum samples and fetal tissue were collected starting October 2012 and tested via ELISA and qPCR. A first wave of Schmallenberg virus infections was detected in 2012/2013 in, and was largely limited to, the southern part of the country. In the second and larger wave in 2013/2014, cases were found throughout most of the country. Since then, no major outbreaks have been recorded.