Reproductive failure has a negative impact on animal production, health and welfare and ultimately rural economies. In Ethiopia, the factors affecting small ruminant reproductive efficiency are inadequately investigated. A cross-sectional survey was done from November, 2010 to May, 2011 to investigate risk factors of reproductive failures including Toxoplasma gondii infection. Analysis of 1372 sera (787 sheep and 585 goats) from 409 flocks using ELISA showed high flock (59.7%) and animal (31.8%) level T gondii seroprevalence. An overall 24.9% (341/1372) annual abortion rate (19.6% in sheep and 32.0% in goats) was recorded. Animal level T. gondii seroprevalence was significantly associated with abortion in Ambo and Ada'a-Liben districts (Odds ratio [OR] = 2.31, 95% confidence interval [CI]: 1.42, 3.76; P = 0.001). Questionnaire survey on 199 households of Ambo, Ada'a-Liben and Fentale districts revealed high flock level abortion (57.5%), still birth (28.9%) and neonatal losses (47.9%), which are significantly different between study districts (P < 0.001). Multivariable logistic regression model showed that species (goat), large flock size, pastoral and agro-pastoral production systems, drinking water from river and stagnant water bodies, grazing/browsing in plain land and extensive management were significant predictors of flock level reproductive failures. In the final Zero inflated Poisson regression model number of abortions was significantly higher in goat than in sheep flocks (Incidence risk ratio [IRR] = 1.42, 95% CI: 1.08, 1.87; P = 0.012). It is also significantly higher in pastoral (IRR = 1.81, 95% CI: 1.16, 2.83; P = 0.008) and agro-pastoral production systems (IRR = 1.94, 95% CI: 1.32, 2.86; P = 0.001) than in sedentary production system. Prevention of toxoplasmosis, improved husbandry practices and further epidemiological studies to identify causes of reproductive failures are recommended. (C) 2013 Elsevier Ltd. All rights reserved.