To establish the differential diagnosis and treatment method in bovine ovarian cysts, specially ovarian cysts with corpus luteum, serum progesterone concentration, rectal palpation and ultrasonography for measuring the cystic wall thickness and diameter of cyst and corpus luteum were investigated from 1,188 dairy cows with ovarian cysts. The plasma progesterone concentrations were 0.3$pm$0.4 (mean$pm$SD) ng/ml in 629 cows with follicular cysts, 3.7$pm$1.1 ng/ml in 431 cows with luteal cysts, and 3.8$pm$1.2 ng/ml in 128 cows with coexist of ovarian cysts and corpus luteum, respectively. The cystic wall thickness by ultrasonography were 1.6$pm$0.4 mm in 629 cows with follicular cysts, 4.2$pm$1.5 mm in 431 cows with luteal cysts, and 1.6$pm$0.6 mm in 128 cows with coexist of ovarian cysts and corpus luteum, respectively. The days from initial treatment to insemination in follicular cysts were 28.1$pm$6.9 days in treatment of GnRH alone, 15.9$pm$2.9 days in combination of GnRH and dinoprost, and 15.1$pm$3.1 days in combination of GnRH and cloprostenol. The percentages of cows conceived within 100 days after initial treatment were 61 %, 68% and 73% in treatment of GnRH alone, combination of GnRH and dinoprost, and combination of GnRH and cloprostenol, respectively. The days from initial treatment to insemination in luteal cysts were 3.8$pm$0.6 days in treatment of dinoprost alone and 3.8$pm$0.7 in cloprostenol alone. The percentages of cows conceived within 100 days after initial treatment were 69.5% and 68.5% in treatment of dinoprost and cloprostenol, respectively. The days from initial treatment to insemination in coexist of cysts and corpus luteum were 3.7$pm$0.7 days in treatment of dinoprost alone and 3.8$pm$0.6 in cloprostenol alone. The percentages of cows conceived within 100 days after initial treatment were 87% and 84% in treatment of dinoprost and cloprostenol, respectively. These results suggest that the best choice for treatment agents in ovarian cysts were combination of GnRH and PGF$_2$$alpha$ in follicular cysts, and the PGF$_2$$alpha$ in luteal cysts and in coexist of cysts and corpus luteum, respectively. In conclusion, it is suggest that ultrasonography is useful diagnostic tool for diagnosis and selection of treatment remedy in cystic ovaries of bovine.