Attorney General Todd Blanche has long maintained that the so-called Epstein files, even those kept from the public, contain no secret information related to national security.
When the document releases began last winter, Blanche noted that the Epstein Files Transparency Act authorized withholding information in the interest of national security or foreign policy, but said, "no files are being withheld or redacted on that basis."
"There's not some tranche of super-secret documents about Jeffrey Epstein that we're withholding, we're actually not withholding anything based upon [national defense information]," said Blanche, who was deputy attorney general at the time.
But the contents of at least three documents in the massive tranche of files indicate classified information was included in files collected by the DOJ.
One of the documents shows Blanche's Office of the Deputy Attorney General itself received classified material related to Epstein in March 2025. By law, material can only be classified for national security purposes.
What exactly was classified and why remains a mystery.
The Department of Justice says it collected 6 million pages of material and ultimately released over 3 million of those pages after reviewing for duplication, attorney-client privilege and relevance to Jeffrey Epstein.
Congressional challenges and a lawsuit are casting doubts on the DOJ's claims and demanding the release of more documents that were held back.
Clues about classified material
Included among the Epstein files is an eight-page timeline of the FBI's New York office's initial efforts last year to track down and deliver its voluminous files to the Justice Department's Washington headquarters.
On March 25, 2025, one document shows delivery of "16 Epstein items to ODAG," referring to the Office of the Deputy Attorney General. Among them, items No. 2 and No. 6 are described as "Epstein Transparency Project - Classified Material" and "CDs with classified materials (x2)."
The Epstein Transparency Project refers to the Justice Department's effort to review the files and redact, withhold or clear them for release. It is not clear what exactly was identified as classified. Each CD was likely capable of holding hundreds of megabytes of material.
Also in the files is an email sent that same day from the unit chief of the National Security Classification Operations Unit — an office whose role is to review FBI documents for classification or declassification. The email includes an attachment labeled "Epstein - Classified Document Memo.docx."
The body of the email says there were three documents "identified that remain classified." One was described as an "FBI document which is classified when see-through." A redaction obscures the unit chief's description of the other two documents.
The identity of the email's recipient is also redacted.
It's also not clear whether the two documents — the email and the list — are referring to the same classified material.
Coding system reveals missing pages
A CBS News analysis of a numerical coding system used by the DOJ to organize the Epstein files offers clues about some of the documents the department has withheld.
The codes don't reveal what's missing, but they do show where gaps exist, raising questions about the DOJ's explanation for why documents were withheld.
Among the missing documents are pages from Epstein's own financial records collected as evidence in a federal prosecution.
Here's how it works: Documents from the Epstein files are labeled with a string of numbers beginning with the letters EFTA stamped on the bottom right-hand corner; EFTA stands for Epstein Files Transparency Act.
Those are called Bates numbers — a common way of organizing massive document batches in legal cases. Every page receives its own number. In the Epstein files, the sequence goes from 1 to 2,858,498, which is the tally of approximately how many pages of documents were released.
According to the DOJ, other documents — including court records and investigative files they've previously released — bring the total to over 3 million.
Alongside the Epstein files' Bates numbers are other, older coding numbers that appear on many documents. This indicates that those documents had previously been used in federal legal cases, potentially collected as part of an earlier subpoena.
For instance, Bates coding on some of the documents is from the Ghislaine Maxwell criminal case and was used to organize files given to Maxwell's legal team ahead of her 2021 trial as part of the discovery process.
Other Bates numbers indicate documents were collected from Epstein's banks, including JPMorgan and Deutsche Bank, during the FBI's investigation into his trafficking activities.
Similar gap analyses have been done in the past by independent researchers.
Missing financial documents
Finding gaps in these documents is a simple process of counting.
In tens of thousands of instances, the main EFTA number will advance by one but the other Bates numbers advance by two or more. Those gaps indicate pages that had been there before were likely removed at some point after the DOJ obtained them.
Take the images below: The EFTA number advances by one but the JPM-SDNY and SDNY_GM numbers advance by 2, as do the page numbers from the original document.
In another example, a series of around 4,500 images of checks from Epstein's accounts has gaps where 66 of those check images should be. Oftentimes the missing image is only the front or the back of the check, although in several cases both are missing.
Comparing all of these numbers against the final EFTA page numbers, it is possible to calculate that there are tens of thousands of pages of documents that are missing from these sections, with no clear reason why.
"Financial records were not a permissible category for removal," Barbara McQuade, the former U.S. Attorney for the Eastern District of Michigan, told CBS News.
Like every federal prosecutor, she says she is very familiar with Bates numbers. "It's the reason you have Bates numbers, so you notice something like that," she said.
The DOJ hasn't responded to CBS News' recent inquiries about the Epstein files, but it has previously said that every document required to be released by the Epstein Files Transparency Act has been released, and the remaining files were unrelated, privileged, or were duplicative.
Email gaps
Another sequence of Bates numbers that provide a map to where documents were removed appears to be from a preliminary processing of the files.
One large sequence of those have "R1" in between EFTA and the page number.
This R1 numbering is found across approximately 995,000 released pages, between p. 61 and p. 2,214,171 in the files. Each page is also labeled with an EFTA page number.
While the EFTAs are sequential, the R1s have gaps which range from 1 page to hundreds of pages. Each time a gap appears — for example, if the EFTA advances by 1 but the R1 advances by 2 — it's evidence that pages were removed.
By comparing these sequences it's possible to identify gaps where documents, mostly emails, were removed between that earlier review and the final release. No partial emails turned up in the thousands of documents we examined, so the removals appear to be entire email exchanges.
Here's what a section of that looks like:
The emails are not sequential in date and jump by days, months and years, so knowing what was removed from context is simply not possible.
But the results of calculating the differences between the first and last of the numbers in this earlier sequence versus the later sequence is 1.2 million pages, which is the total number of identified gaps from just this one section.
Most of the documents in this section are emails to or from Jeffrey Epstein, including communication with young women who would later accuse him of abuse; email exchanges with his business associates; messages to or from his assistant, Lesley Groff; or emails sent or received by Ghislaine Maxwell.
"De-duping"
There is one possible explanation for many of the email gaps. Instructions given to DOJ attorneys working on processing the redactions state:
"If the document is an email chain and the most-inclusive email (i.e., containing all the back-and-forth) has already been reviewed and redacted as appropriate for production, the interstitial back-and-forth can be marked as duplicates."
In other words, all emails exchanged prior to the last email in a chain can be considered a duplicate, because the last one should include all of the messages, and eliminating the duplicates will speed up the redaction process. Once a document is marked as a duplicate, it would likely be excluded from the files.
If that was the case, this was only partially accomplished because duplicate emails still exist throughout the files.
There's also the possibility that errors in the process could have resulted in crucial emails mistakenly being deleted.
Lack of transparency
The review and redaction process was conducted by hundreds of DOJ attorneys working under a compressed timeline. Given the scale of the task, it's possible that pages were withheld as a result of honest mistakes. But without a roadmap to the redactions and removals, it's impossible to make that determination.
Independent journalist Katie Phang is suing the Justice Department, seeking the release of more files as well as an explanation of redactions and removals. A federal judge has made several rulings in her favor and the DOJ is appealing those rulings.
As part of her lawsuit, Phang is asking the court to appoint a special master to review the files.
"If it wasn't intentional, then was it gross negligence? Were you just lazy? If it was intentional then I think there's [expletive] there that they don't want people to see," Phang told CBS News. "My speculation runs an entire spectrum of reaction — but at the end of the day it just makes the DOJ look bad."
The DOJ has acknowledged making several mistakes.
It admitted to removing, and then restoring, a photo of now Commerce Secretary Howard Lutnick on a 2012 visit to Epstein's island, contradicting claims Lutnick had previously made about his contacts with Epstein.
Last year, DOJ officials claimed a minute was missing from prison security video from the night Epstein died, which turned out to not be true.
"This is a case where the process has inhibited public trust in what is ultimately released, and there's a long tradition of this, whether it's the Pentagon Papers or the Epstein files," said attorney Stanley Brand, a veteran litigator and distinguished fellow in law and government at Penn State Dickinson Law.
"This is just another piece where the government process, where making this stuff available just fuels suspicion that there's something we're not seeing, and I don't know that ever gets resolved."
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