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Over the years a variety of different numbering systems have been employed by Edison and others to identify the notebooks used at Menlo Park and the later laboratories. Affixed to the front cover of most of the standard-size Menlo Park notebooks is a label containing the inscription: "From the Laboratory of T. A. Edison. Menlo Park, N. J. No. _____." The numbers themselves run from 1 through 249 and were probably assigned to the books before they were put into use. The numbered books do not progress in strict chronological order, and related books sometimes contain widely separated Menlo Park numbers. About seventy of the numbered notebooks are missing from the collection at the Edison National Historical Park. There are also a few notebooks whose damaged labels obscure any numbers that might once have been affixed to them. This is the only numbering system that was consistently in use during the time the books were being used in the laboratory and, for this reason, the books are arranged in the order of their Menlo Park number.

Many of the Menlo Park notebooks also contain a second numbered label affixed onto the front cover several inches above the Menlo Park label. These labels were probably added to the books during the 1890s at the time they were sent to the General Electric Board of Patent Control in New York City. With only a few exceptions, all of the books containing the second numbered label also have the Board of Patent Control's bookplate pasted onto their inside front covers.

For the first thirty-four Menlo Park notebooks, the two sets of numbers are identical. Thereafter, the second set of numbers progress in the same sequence as the Menlo Park numbers, but many of the notebooks lack the second number and the General Electric bookplate. Menlo Park Notebook #249, the last numbered book in the series, also has a second label bearing the number 147. Similar labels appear on a few other notebooks. Two of the New York notebooks are numbered 148 and 149. The six pocket notebooks used by Charles P. Mott are numbered 150-155, and one other pocket notebook is numbered 156.

Unlike the Menlo Park notebooks, the notebooks used at the laboratories in New York, Fort Myers, and the Harrison lamp factory do not contain a standard printed label or a standard notebook number. Some of these books, however, do have a small numbered label affixed to their spines. The numbers range from 23 to 35. Many of the Menlo Park notebooks lacking the General Electric bookplate contain similar labels, with numbers ranging from 2 to 22. These numbers were probably affixed to the books after Edison's move to West Orange in 1887. Over 100 books with these small numbered labels are found among the West Orange notebooks. Book 1 and Book 36 both date from 1887.

Beginning in the late 1930s, the archivists at the West Orange Laboratory began assigning "N-numbers" to the standard-size notebooks used by Edison at Menlo Park and the later laboratories. A similar number with the prefix "PN" was assigned to each of the pocket notebooks. This six-digit number corresponds to the first dated entry in the notebook. For example, a notebook whose first dated entry was for November 9, 1878 would carry the number N-78-11-09. Unfortunately, this number is not always a reliable indicator of the date when a book was first used. Many of the books were in use for a long period of time before any entry was dated, and hundreds of other books contain no dated entries. Moreover, subsequent research has revealed that many of the supplied or conjectured dates are inaccurate. For these reasons, the N- or PN- number should never be used as the basis for dating a notebook.