The vast majority of Pauling's work during World War II was classified under U.S. and British anti-espionage laws. As a result, it was sometimes difficult for Pauling and other scientists to communicate with one another and share ideas without breaking certain OSRD-established regulations. Even more troublesome were the screening and registration processes that were required when sending restricted information by mail. Senders and recipients had to be authorized to handle said information, letters had to be approved, and the sending and receipt of the items needed to be documented by OSRD staff. In order to circumvent these cumbersome regulations, the OSRD-employed scientists often exchanged letters alluding to but not directly referencing specific projects. These documents read much like transcripts of conversations between savvy criminals, often referencing "the project", "a known chemical", or in the more informal letters, "the thing." One can read the occasional wink or smirk behind these letters as the civilian scientists flouted strict government laws in favor of maintaining the open, communal air of the American scientific collective.

In some cases, even reports to the OSRD were too important to contain specific details. In one letter, Pauling references a "silver physical reagent," something he notes that the Office of Censorship has some experience with. In fact, the fear of espionage was so great that it sometimes boiled over into misplaced accusations and investigations. In one case, a document relating to work done in the Caltech labs disappeared in transit to an East Coast lab. Following several accusations from a military officer, the missing document was located, having been misfiled at the recipient's office. Though Pauling was not directly involved in the drama, as an Official Investigator at Caltech he received several letters regarding the incident, one which hinted at suspicion of treason.

A portion of the documents housed in the Ava Helen and Linus Pauling Papers were, at one time, registered as classified information by the United States government. Though a large number of the World War II-era documents have been classified as "restricted", "confidential" or "secret", the final classification denoting documents of highest sensitivity, "top secret", cannot be found in the collection. It does not appear that Pauling worked on any project termed "top secret" during his time with the NDRC or OSRD.

Among the most interesting secret documents in the Pauling collection is a series of items relating to his work with invisible inks. The documents themselves, mostly reports to the OSRD, are largely vague and offer little specific information. What makes them interesting is the possibility that they may be closely related to some of the oldest classified documents in the United States National Archive. The National Archives currently hold six classified documents dating from 1917 - the time in which Arthur Lamb, an associate of Pauling's, was first engaged in work with invisible ink - which contain explicit information on invisible ink and a 1945 "Secret Ink Technical Manual." While Pauling does not appear to have personally owned copies of any of these documents, it is likely that through his work with Lamb, he may have been familiar with the contents of the items from 1917 and may have contributed to the information compiled in the 1945 manual.

While our knowledge of Pauling's work may today be in some ways limited by concerns for national security, it is likely that the items held in the National Archives will eventually be declassified, perhaps allowing us a better understanding of the role that Pauling and his colleagues played in the outcome of World War II.

It should be noted that the Oregon State University Libraries Special Collections has received explicit permission to make all documents in the Ava Helen and Linus Pauling Papers with a classification level of "secret" or lower available to the public.