Dual-process theories may be invoked to explain how physicians interact with, interpret, and draw inferences from clinical information. Stanovich and West's model articulates two kinds of thinking--intuitive-based System 1 and analytical-based System 2--which have been under-investigated with physicians in training. This qualitative study explored pre-clerkship medical students' retrospective perspectives and experiences of System 1 and System 2 thinking via 12 semi-structured interviews and abductive, progressive focusing. Participants identified patient interactions, clinical note writing, knowledge synthesis, problem list and differential diagnosis generation, evaluating evidence, and critical appraisal of literature as pre-clerkship opportunities to engage in System 1 or System 2 thinking. Six major themes emerged from analysis of participants' interview transcripts: cognitive processes, deliberate practice, learning environment: being alone or being together, stickiness factor, biases and heuristics, and prior experience of attaining competence. Participants valued the anticipated role that System 1 and System 2 thinking will play in their future practice, and experienced nascent, self-regulated development of these cognitive processes during the pre-clerkship phase of their education without formal feedback or coaching from clinician preceptors. Pre-clerkship curricula should further embrace low-stakes, incremental teaching on metacognition and continuous monitoring of knowledge processing as a key competency for physician learners.