With his conception of critical code studies, Mark Marino aims to persuade people—"artists, practitioners, and scholars"—of the cultural significance of source code and the need for analysis and interpretation of source code as text. His 2006 essay “Critical Code Studies” in Electronic Book Review started the development of Critical Code Studies in a reflective, theoretically grounded manner, which over time has grown into a "collection on methods and discourse" (Marino). In that essay, Marino argues that: "Critical Code Studies (CCS) is an approach to code studies that applies critical hermeneutics to the interpretation of computer code, program architecture, and documentation within a sociohistorical context. CCS holds that the lines of code of a program are not value-neutral and can be analyzed using the theoretical approaches applied to other semiotic systems, in addition to particular interpretive methods developed specifically for the discussions of programs. Meaning grows out of the functioning of the code but is not limited to the literal processes the code enacts. Through CCS, practitioners may critique the larger human and computer systems, from the level of the computer to the level of the society in which these code objects circulate and exert influence."

Critical Code Studies' emphasis on close reading makes it especially well-suited for case study research. Several applications of Critical Code Studies have led to books, such as Reading Project: A Collaborative Analysis of William Poundstone’s Project for Tachistoscope {Bottomless Pit} which combines Critical Code Studies with quantitative cultural analytics and close reading of the interface to insight into one work of electronic literature. Moreover, the book 10 PRINT CHR$ (205.5+RND(1)); : GOTO 10, contains ten analyzes by different authors of the same one-line Commodore 64 BASIC program. Marino's 2020 book Critical Code Studies contains six chapters of case studies as well as a revised manifesto and a look to the future of the field.

Although not a methodological requirement, the application of Critical Code Studies is often characterized by a collaborative approach. Marino and Jeremy Douglass organize biennial Critical Code Studies Working Groups which started in 2010. Through various themes, participants have collaborated on analyzing various case studies. Marino’s approach puts into practice what he argues in Critical Code Studies: Critical Code Studies is a field for amateurs and professionals of various fields, as long as they are interested in the cultural reading of source code. This open social scholarship approach sets up the public forum as a conversation about code, highlighting the layers and ambiguity of any piece of code. The working groups include personal readings of participants but add up to a greater role of generative interaction between participants.