The good news is that historians and other parties now have a treasure trove of Cold War era history available to them in released CIA documents, housed on line in a variety of repositories including the Mary Ferrell Foundation and Black Vault.
However anyone reading them will be faced with the reality that CIA documents contain a variety of code words, all of which are designed to conceal and protect critical information about operations, employees and assets in the event that the documents themselves would be “compromised”. That means having them obtained by anyone outside the intelligence agency, whether it be an adversary power, the media, or any party outside the service itself. This security practice also concealed that same information from other agencies, law enforcement and the military, who are routinely copied on certain types of CIA memoranda and reports.
The Mary Ferrell Foundation now offers an extensive guide to decoding CIA cryptonyms of the 1950s and 1960’s, and we are working on a project to add other related operational security categories such as pseudonyms and aliases. I’m working on an overview to address the larger spectrum of document security “tradecraft” including personnel security (aliases, backstops, covers), but for now I thought sharing the following might be helpful in differentiating cryptonyms from pseudonyms.
The first and most common mechanism of operational and personnel security has been to assign code names (cryptonyms) to functional sections of the CIA itself, to its offices and facilities, and to other government agencies as well as to its own operations and personnel. .
To simplify matters and control document routing, the first two digits in the cryptonym’s/codes normally refer to the geographic or functional area of a particular directorate, geographic region, office, or operation. The rest of the code name was intended to be meaningless although that appears not to have been true in all instances. In some cases the codes seem show a bit of “attitude” – such as designating ODENVY to refer to the Federal Bureau of Investigation, ODYOKE as a general code for the U.S. government, or ODACID for the State Department.
Protocol called for the code names to be centralized and registered but in practice some groups – such as counter intelligence – had the authority to create and control their own codes, and even maintain their documents outside the centralized system during certain periods of time.
In some instances code names for operations were also extended to individuals involved with them (usually individuals who were operational assets or parties of interest and not CIA personnel), creating an entire series of cryptonyms – AMOT-1, AMOT-39 etc.
While cryptonyms were used for organizational and operational security, other types of codes and measures were used to protect the identity of individual CIA employees or, on occasion, a contact working as a source for the CIA whose “true name” required concealment. Pseudonyms for CIA employees were often assigned for their entire career, while others were limited to the period in which the individual was working with the agency, either as a volunteer or assigned by their respective organization. That held true for both civilians and military personnel “detailed” to the CIA from a particular service. CIA contract employees could also be assigned different pseudonyms over time.
Pseudonyms were registered and were restricted to use in reports, memoranda and other document related activity – not to be used externally.
Individuals who did need to present themselves in public, using assumed identities for different operations and activities, were assigned false names and in some instances extensive false identities – the names and identities were assigned as “aliases”. Aliases would be regular names, some of them similar to true names but others strikingly different. We do find aliases mentioned in documents; in some instances “true names” are also given to help with the obvious internal confusion.
Aliases that were used for any extended period of time had to be “backstopped” with residence and mailing addresses, as well as other precautions to ensure that the individual using them would be able to function using a name and identify other than their true name. Short term aliases generally involved at least a minimal level of false identification and miscellaneous but related materials sometimes referred to as “pocket litter”.
Individuals detailed to work with the CIA on covert action projects were assigned certain types of “covers” for operational security, the most basic being that of an employee of another government agency such as the State Department or USAID; the simplest covers were little more than mailing addresses where mail could be received under one name and forwarded to another – or simply forwarded as a routine forwarding request. An example would be to have military personnel detailed to serve in the earliest years of the Vietnam era forwarded or returned from a military postal address in the Philippines.
Clearly this all got quite confusing, even internally within the CIA, and we do find documents with handwritten annotations of true names beside pseudonyms or even aliases, a security violation but still a temptation for those trying to deal with reams of reports and memoranda.
Larry Hancock 
Makes you wonder how senior managers kept fully aware of their own operations.
One of the true risks of covert action is that the most senior managers often had a limited knowledge of field operations. It quickly became standard practice to shield the president from a certain level of detail, leaving that to the variously named special oversight groups. Dulles is even on record as advising the Cuba Project special group not to discuss certain things with the president in the interest of deniability – the national security advisor served as a buffer.
But beyond that field personnel themselves appear to often have observed the same rule, especially it the mission began to run into difficulties and they had to do things that HQ probably would not sanction. I’ve written about several examples where station chiefs ordered things not to be covered in reports, especially if HQ had advised against them – during the efforts against the Russians in Afghanistan the station chief in Pakistan told his people to stop telling HQ about providing IED materials / training and advanced sniper weapons – that certainly did not end well.
Compartmentalization and deniability breed loss of control, its the nature of the beast. I’m writing about that in great detail in regard to the Cuba Project. As an example the military chiefs of that project later went on record that the senior officers – Bissell and Barnes did not know enough detail to brief the incoming Kennedy administration, yet Bissell actually removed them from key meetings.
It’s a real mix, sometimes the senior officers simply did not know details, on other occasions they seem to have avoided them for political expediency.