Late-term abortion, stillbirth, and neonatal foal mortality (commonly referred to as late fetal losses [LFLs]) of unknown etiology are a serious concern for horse farmers and breeders in Kyrgyzstan. Therefore, we investigated major infectious causes of LFL, with a focus on viral agents, for the first time in the horse population in the country. A total of 221 sera and 149 nasal swabs taken from mares in farms with a history of LFL within 1 year of testing as well as tissue samples collected from 17 LFL cases were investigated. Serologic studies revealed that equine herpesvirus type 1 (EHV-1) and type 4 (EHV-4) were prevalent in the population, although positivity rates were low with neutralizing antibody titers of 1:4 to 1:32 (median 1:8) against both pathogens. High antibody titers in the range from 1:32 to 1:512 (median 1:256) against equine arteritis virus (EAV) were detected in mares on a single farm, whereas three mares from different farms tested positive for Dourine. Virus isolation and PCR investigations of nasal swabs did not suggest ongoing active infection with EHV-1, EHV-4, or EAV in the examined mares. Bacteriologic and virological examination of tissue samples taken from LFL cases revealed the presence of Escherichia coli and/or Streptococcus equi (subsp. zooepidemicus) in 35% of neonatal foal death cases, and EHV-1 was isolated from a late-term abortion case representing the first isolation of this important pathogen of horses in the country and, to the best of our knowledge, in Central Asia.