A good reproductive performance is a central element of animal breeding. The breeders of Entlebucher Mountain dogs observed a decrease of the mean litter size and an increase of the number of unsuccessful matings in the past years. The aim of the present study was to identify factors with an influence on fertility in this breed. In total, 915 litters from 202 sires and 348 dams from 1986 to 2013 entered the analyses. The total puppy losses (7.4%) reduced the mean litter size at birth of 5.49 ± 2.13 to a mean litter size at registration of 5.08 ± 2.05. There was no deviation from the expected equal sex distribution for puppies at birth and at registration, as well as for puppy losses consisting of stillborn puppies and puppies which died or had to be euthanized before registration. The mean annual litter inbreeding coefficient increased from 0.37 in 1986 to 0.40 in 2013 and was correlated with the year of birth of the litter (Kendall's tau b = 0.46). The age of the dam and parental inbreeding were identified as significant predictors with a negative effect on litter size at birth. For the litter size at registration the age and inbreeding of the dam had a significant negative effect and a 1% increase of dam inbreeding is expected to decrease the litter size at birth and registration by 0.1 and 0.09 puppies, respectively. The occurrence of total puppy losses decreased during the years and was more frequent in larger litters. In addition, in litters of older parents the occurrence of puppy losses was more frequent than in litters from younger parents. The final generalized linear mixed-effects models for litter size at birth, litter size at registration and for total puppy losses explained 36%, 33% and 22% of the total variance, respectively. The impact of inbreeding and parental age on fertility of the Entlebucher Mountain dog was small and the influence of the dam was much bigger than the one of the sire. Other factors must be responsible for the variability of litter sizes not explained by the models. Without changes of breeding circumstances, a further increase of inbreeding must be expected. Therefore, a close monitoring and minimizing of inbreeding must be followed up by the breeding community.