BACKGROUND: The preliminary survey made about congenital goiter in goats in Garmsar township indicated that the disease occurs much more in Beetal-cross than native goats raised in the same area. OBJECTIVES: The aim of the present study was to compare of serum triiodothyronine (T3), tetraiodothyronine (T4) and thyroid stimulating hormone concentrations in pregnant and lactating Beetal-cross and native goats in Garmsar township. METHODS: One hundred Beetal-cross (n=50) and native (n=50) does in 4 groups (25 pregnant Beetal-cross, 25 lactating Beetal-cross, 25 pregnant native and 25 lactating native) were used in this study. Blood samples were obtained via jugular venipuncture and analyzed for serum T3, T4 and TSH concentrations. RESULTS: Breed had a significant (P<0.05) effect on T4 concentration and pregnancy had a significant (P<0.05) effect on T3 and TSH concentrations. No significant differences were seen for serum T3, T4 and TSH concentrations between pregnant and lactating native does. However, in the pregnant Beetal-cross, serum T3 and T4 concentrations were lower (P<0.05) and TSH concentration was higher (P<0.05) than lactating Beetal-cross does. CONCLUSIONS: The results of the present study highlight the relationships between thyroid activity and breed in the goat species that may play a role in more occurrence of congenital goiter in Beetal-cross in Garmsar township.