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In the present study, late term abortions in 477 (17.9%) of 2651 pregnant ewes and 129 of 680 pregnant goats (18.9%) from 17 small ruminant flocks of the South Khorasan province, east of Iran were investigated. Multistage cluster sampling technique was used to select the flocks and aborted animals. From which, 25 appropriate fetuses were chosen for bacterial and fungal contaminations. Blood samples were also taken from forty aborted and forty healthy age matched sheep. No microbial or fungal agents were detected in 45.4 % and 42.8% of sheep and goat,s fetuses respectively. The bacteria isolated from aborted fetuses of sheep and goat´s were as follows: Escherichia coli 27.2% and 7.1%, Staphylococcus spp. 9.0% and 7.1%, Campylobacter fetus 9.0% and 14.2%, Staphylococcus spp. and Campylobacter fetus together 9.0% and 0.0 %, Klebsiellas 0.0 % and 21.4%, Aspergillus fumigatus 0.0 % and 7.1%, respectively. The concentrations of total tri-iodothyronine (tT3), total thyroxin (tT4), copper, phosphorus and magnesium were significantly lower, but thyroid stimulating hormone (TSH) was higher in the aborted ewes compared to the healthy controls. The serum levels of calcium, zinc and vitamin E were not significantly different between the two groups. In conclusion, deficiencies of tT3, tT4, copper, phosphorus and magnesium, and increase in the TSH concentration could have taken part in the etiology of abortion in ewes. The most important cause of late term abortions was probably due to the maternal deficiencies (for example, iodine) in the concurrent drought in the province.