At least four complete volumes and around seven pages of text are missing from Dodgson's 13 diaries. The loss of the volumes remains unexplained; the pages have been deliberately removed by an unknown hand. Most scholars assume the diary material was removed by family members in the interests of preserving the family name, but this has not been proven. All of the missing material, except for a single page, is believed to date from the period between 1853 (when Dodgson was 22) and 1863 (when he was 32).

Many theories have been put forward to explain the missing material. A popular explanation for one particular missing page (June 27, 1863) is that it might have been torn out to conceal the fact that Dodgson had proposed marriage on that day to the 11-year old Alice Liddell. However, there has never been any evidence to suggest this was so, and a paper that came to light in the Dodgson family archive in 1996 provides some evidence to the contrary. This paper, known as the "cut pages in diary document", offers a brief summary of two missing diary pages, including the one for June 27, 1863. It states that there was gossip circulating about Dodgson and the Liddell family's governess, as well as about his relationship with "Ina", presumably Alice's older sister, Lorina Liddell. The "break" with the Liddell family that occurred soon after was presumably in response to this gossip. An alternate interpretation has been made regarding Carroll's rumored involvement with "Ina": Lorina was also the name of Alice Liddell's mother. The reason for the break has never been made clear.

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