The Lee family papers reflect the activities of four generations of one of Salem's prominent maritime families. Included are merchant and shipbuilding papers of Captain Joseph Lee (1774-1831), personal and miscellaneous business papers of commission merchant John Clarke Lee (1804-1877), and business, personal, and estate papers of other Lee family members. While the collection does not contain the papers of Henry Lee (1782-1867), who was an important commission merchant, Calcutta agent, and West Indies merchant, the collection does contain information regarding some of Henry's joint shipping investments with this father (Joseph Lee). The collection has been divided into four series.

Series I. Captain Joseph Lee (1744-1831) Papers documents his business as a shipbuilder, covering the years 1796 until 1831. Located in this series is correspondence regarding orders for ships, legal agreements with clients and workmen, accounts and receipts for construction materials, memorandums of ship dimensions, and drawings of hulls and ship decorations. Joseph's correspondence also includes letters concerning farming and merchant correspondence, circa 1809 until 1810, which reflects Joseph's and his son, Henry Lee (1782-1867)'s, joint investments in Calcutta goods. Of interest are letters, circa 1811, in which Joseph states his distaste of Napoleon and the thought of war with Great Britain. It should be noted that this series does not contain papers of Joseph's important mercantile trade with the West Indies and Spain, papers of his ships, his distillery or his project to build the Essex Bridge.

Series II. John Clarke Lee (1804-1877) Papers contains correspondence, legal and financial papers, and photograph albums, which cover the years 1813 until 1865. Aside from personal letters received from his children, John's correspondence contains letters regarding his financial interests in manufacturing companies, banks, and railroads. There is also correspondence pertaining to gardening and orders for trees. Among the financial and legal papers can be found materials generated from John's trusteeship of Pickering Dodge's estate, including a copy of Dodge's will. The financial papers also contain a number of bills and receipts for Lee's home furnishings. There are two photograph albums which contain the occasional typewritten explanatory notes and photographs of John's residence at 14 Chestnut Street in Salem. These photographs include views of the house's interior and exterior, shots of the garden, and individual photographs of furniture, silver, glassware, ceramics, jewelry, and fans. This series does not contain the papers of the firm, Lee, Higginson and Company.

Series III. Family Papers consists of business, personal, and estate papers of numerous members of the Lee and Rose families (see Appendix III, Select Genealogy). Included are: the will and estate inventory of Nathaniel Cabot Lee (1772-1806); memorandum/diary books of farmer Joseph Lee (b. 1773); financial and estate papers of Harriet (Paine) Rose, whose business interests were often overseen by her son-in law, John Clarke Lee and Rachel W. Rose's estate papers, which were managed by executors Harriet Rose and John Clarke Lee. Also included are personal correspondence, financial papers and a photo reproduction portrait of Harriet (Rose) Lee; Civil War correspondence to William P. Lee (1833- ), who was an agent aboard the Union Army steamers Pembroke and Cambridge; and correspondence, legal, and financial papers of other Lee family members. The papers of miscellaneous family members include a small number of shipping papers of Boston merchant Joseph Lee (1770-1845), as well as a personal signed letter to Harriet Rose Lee (1831- ) from Theodore Roosevelt (1880), and one from Booker T. Washington (1914).

Series IV. Miscellaneous Papers consists of non-Lee family correspondence, legal, financial, and shipping papers ranging from 1680 until 1917. The bulk of the correspondence is of a personal nature including letters to Martha N. Very regarding her charity work in the 1860s, correspondence to Henry M. Brooks, and letters concerning genealogy. Among the legal papers is a 1780 deed for a share in the prizes of the privateer Phenex (Brigantine). Miscellaneous shipping papers contain a ship and cargo listing of "Exports of America, 1804," an undated extract from the journal of the Persia (Ship), and miscellaneous invoices and memorandums. Miscellaneous papers include memorandums and drawings for a house in Northfield, and passports of Edward C. Wilson.