As early as 1754, the colonial government of New York established quarantine measures. A tax was imposed upon all seamen and passengers entering the port of New York, and with the fund thus provided, hospital buildings were established, first on Governor's and afterwards on Bedloe's Island. The establishment was removed to Staten Island about 1799. The tax thus collected from passengers and seamen was paid into a joint fund, under the control of the Commissioners of Health of the city of New York, and called the "Mariner's Fund." The funds thus created, besides providing the quarantine accommodations, were disposed of by the Legislature in establishing city dispensaries, assisting the Society for the Reformation of Juvenile Delinquents, etc., etc. The manifest injustice of taxing seamen for quarantine purposes, and in distributing their hard earnings among other charities in which they had no special interest, was discovered by commercial men of New York over forty years ago, and an effort was made to abolish this long-standing abuse. The Legislature of 1831 created a board a trustees to collect these funds and employ them exclusively for the benefit of seamen. It was believed at that time that over three hundred and forty thousand dollars had been paid by passengers and seamen into the fund, above what had been used for their benefit, and the money still on hand at that time they were authorized to receive from the State treasury, which amounted to over twelve thousand dollars. The first meeting of the board of trustees of the Seamen's Fund and Retreat was held at the Mayor's office, May 9, 1831, and measures were soon taken to maintain all diseased seamen in the Marine Hospital, Staten Island, and in the New York Hospital. After examining several farms on Staten Island, the trustees purchased forty acres of land of Cornelius Corson, fronting on the New York bay, for $10,000. The land contained a farm-house, to which it was proposed to add an additional building for the reception of patients. The new hospital in process of erection on the summit of the elevation was overtaken with a storm so violent as to throw down its brick walls when they were nearly completed. On the 12th of June, 1832, the executive committee reported the completion of the new building, and about the middle of the following month it was occupied. As the accommodations continued inadequate, a plan was formed for the erection of the main buildings now in use, which are situated much nearer the shore.

The corner-stone of the present hospital was laid July 4, 1834, by Samuel Swartout, Esq., collector of the port, and president of the board of trustees, assisted by the architect, Mr. A. P. Maybee. The address was delivered by the Rev. John E. Miller, Rev. Henry Chase, pastor of the Mariner's Church, and other clergymen assisting in the services. This hospital consists of a main structure fifty feet square and three stories high, with two wings each seventy-six by thirty-four feet, built of hammered blue stone, trimmed with granite, and covered with brazier's copper. The central building and south wing were completed in January, 1836, and the north wing in 1852.