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Writing scientific articles is a daunting task for novice researchers. In this qualitative study carried out in 2007, the authors evaluated the experiences of a group of novice researchers engaged in the writing process, to elucidate the main difficulties and sources of encouragement they encountered.Sixteen novice researchers were interviewed. Most were women (10), and most were enrolled in programs of medicine (9), followed by nursing (4) and physical therapy (3). These were drawn via convenience sampling from a randomized control trial in which 48 of them were equally assigned to either an online or a face-to-face course of instruction. On completion, interviews were conducted in focus groups of four students each. The interviews were transcribed and read independently by two of the authors, who then encoded the material based on the principles of grounded theory. Initial categories were converted to major emerging themes, which were validated when participants were asked to review the findings. Triangulation of results was carried out by discussing the emerging themes in an online forum with five specialists in college writing education.Classifying the diverse responses of participants led to the emergence of four major themes: cognitive burden, group support and mentoring, difficulty in distinguishing between content and structure, and backward design of manuscripts.The themes produced by this study provide some insight into the challenges faced by novice researchers in their early attempts at scientific writing. Remedies that address these challenges are needed to substantially improve scientific writing instruction.