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Rh 1, 1869. For the next succeeding four years he was superintending engineer of the tenth lighthouse district, when he was again assigned to General Sheridan's staff for the purpose of making a series of surveys, embracing the battlefields of Winchester, Fisher's Hill, Cedar Creek, Dinwiddle's Court House, and other historic sites, in connection with Sheridan's campaigns in the Shenandoah region.

From May 9, 1877, to July 12, 1878, Colonel Gillespie was on leave of absence, in Europe. Upon his return, he superintended the surveys and improvements of rivers and harbors in Oregon, and the defenses at the mouth of the Columbia river, as well as the thirteenth lighthouse district. He was stationed in New York city, from 1881-86, in charge of the river and harbor improvements and interior defenses of New York harbor; and from 1886 to 1888, he was in temporary charge of the improvements of New York harbor, the Hudson and Harlem rivers; Raritan Bay, New Jersey; East River, Hell Gate, and other riparian projects, at the same time supervising the East River bridge. During the succeeding years he had charge of the defenses at Fort Hamilton, New York, and Sandy Hook, New Jersey, and was a member of the board of engineers of the United States army. In 1892 he completed the plan for the fortification of the lower bay, New York, and in 1894 emplanted the gun-lift battery at Sandy Hook, the first designed in this country for modern armament. In 1895 he was made president of the Mississippi river commission, and was chiefly responsible for the selection of Galveston, Texas, and San Pedro, California, as deep-water harbors.

During the Spanish-American war, in 1898, he was appointed brigadier-general of volunteers and assigned to command the department of the East, with headquarters at Governor's Island, New York. In 1900, he visited Porto Rico, as a member of the board of officers to determine what lands were necessary for military and naval purposes of the United States. He received the appointment of chief of engineers of the United States army, with the rank of brigadier-general, on May 3, 1901. He is president of the Board of Ordnance and Fortifications, and a member of the Army War College Board of Washington, District of Columbia.