Morgan's scholarly nephew Junius encouraged him to collect early printed books and illuminated manuscripts. Notable individual purchases included the splendid Lindau Gospels, Morgan's first major manuscript acquisition, and the very rare Mainz Psalter of 1459. Morgan became a serious collector of drawings later in life, when he purchased the Charles Fairfax Murray collection in 1909. Comprising roughly fifteen hundred works dating from the Renaissance to the eighteenth century, it is generally regarded as the first classic collection of old master drawings in the United States and formed the core of the Morgan's holdings.

In general Pierpont Morgan's collecting proclivities followed accepted patterns of the day, favoring the older periods and schools of Western Europe. In 1911, for example, he purchased most of the group of some sixty Coptic manuscripts that had been discovered the year before in the ruins of a monastic library near the Egyptian village of Hamouli in the Fayum.

In collecting autograph manuscripts, Morgan also sought many of the most popular figures of his own time—including Charles Dickens and Mark Twain, from whom he directly acquired the manuscript of Pudd'nhead Wilson in 1909.

An unconventional interest was manifested through his impressive collection of ancient Near Eastern cylinder seals, which at his death numbered upward of twelve hundred. Today the Morgan's seal collection is one of the world's most important. He also acquired fine cuneiform tablets, most of which are now in the Babylonian Collection that he founded at Yale University.