The majority of the notebooks are A5 or similar. Most of the content is handwritten unless specified otherwise.
Many of the notebooks contain transcriptions of hieratic texts from ostraca, papyri and other objects. Also recorded are transcriptions of graffiti (hieratic and hieroglyphic) and hieroglyphic texts from monuments.
Texts were often copied in situ at sites or in museums and were continually collated. Transcriptions were also made using photographs and publications as source material.
Some notebooks are thematic focusing on economic and social history issues. These subjects include Egyptian administration (nomes), prices, topography (e.g. Deir el-Medîna), etc.
Notebooks compiled from material consulted in Egyptian collections, mostly in European countries and Egypt. Černý visited museums with major collections of hieratic material from Deir el-Medîna, most notably, Museo Egizio, Turin; British Museum, London; [Ägyptisches] Museum, Berlin; and Rijksmuseum, Leiden.
Černý compiled a series of slip-indexes for the transcriptions (slip-indexes, see Černý MSS 23 to 46).

867 groups of documentation, mainly for ostraca with hieratic inscriptions, as well as a small number of ostraca with demotic or Coptic inscriptions, or ostraca with figures.
Writing boards with hieratic inscriptions are also included.
Most of the documents are photographs. The rest of the material includes transcriptions, translations, facsimiles, correspondence, annotated off-prints and various notes.

-Museums, Černý MSS 1.1-522 (523-4, numbers not allocated)
-Collections, Černý MSS 1.525-594
-Not identified, Černý MSS 1.595-625
-Miscellaneous, Černý MSS 1.626-830

277 groups of photographs. Most black and white images. Series includes photographs taken at sites including wall scenes in temples and tombs, and objects in museums, private collections, seen with dealers, location not known and not identified:
-91 groups for sites and wall scenes, Černý MSS 2.1-184, 405-416
-182 groups for objects in museums, private collections, dealers, location not known and not identified, Černý MSS. 2.185-400, 2.417-725
-2 photographs of Oriental Congresses: 1928, Černý MSS 2.401; 1931, Černý MSS 2.402
-2 photographs of Egyptologists: Ludwig Keimer, Černý MSS 2.403; Adolf Erman, Černý MSS 2.404

48 groups of documents, handwritten and typewritten manuscripts.
Drafts and preparatory notes for both published and unpublished articles. Texts of lectures.

245 groups of documentation for papyri with hieratic inscriptions, and a small number of papyri with demotic inscriptions.
Most of the documents are photographs. The rest of the material consists of transcriptions, translations, colour transparencies, facsimiles, photostats, annotated off-prints, various notes, and a card index for Deir el-Medina papyri.

-Museums, Černý MSS 3.1-283, 3.300-777
-Private collections, Černý MSS 3.778-780, 782-792
-Location not known, Černý MSS 3.792A
-Miscellaneous groups and unidentified locations, Černý MSS 3.794-812
Subsections within series:
-Oracular amuletic decrees, Černý MSS 3.826-875
-Abusir papyri, Černý MSS 876-888
-Love poetry, P. Chester Beatty, Černý MSS 3.781, 793.1-5
-Other love poetry texts, Černý MSS 3.793.6-793.16

38 groups of records and notes on graffiti, including tracings, transcriptions and maps.
Notes and indexes mainly for Theban graffiti and the Nubian graffiti.
A set of proofs for a part of Graffiti de la montagne thébaine.
The Theban material largely covers work on the Theban mountain in the 1960s and includes preparation of graffiti lists for publication.
There are also some graffiti Černý consulted for A. J. Arkell in the late 1940s/early 1950s.

36 groups of material on translations, commented translations and notes.
Translations mainly of papyri and monuments.

Professional and personal correspondence, the majority of letters date between 1946-1970 and are addressed to J. Černý in London, Oxford, Prague and other European, American and Egyptian addresses and locations. The letters contain Egyptological information regarding text readings, translations, exchange of information on objects in museums or in situ, sites and texts.