Ninety-Nine Lessons in Critical Thinking was designed to enhance the reader's awareness of how they think and how decisions involving patients and scientific matters can be influenced by word choice, preconceived ideas, framing, biases, and inattentiveness. Entertaining and informative stories from the author's 45 year clinical and scientific experience and from the history of medicine and science are presented to illustrate ways in which critical thinking skills can be developed and awareness of thought processes enhanced. The evolution of human learning and awareness is used to illustrate the fundamental nature of the concepts, and emphasis is placed on ways to enhance awareness of how our attention and words influence thought. Medical professionals (including medical students, residents, postgraduate fellows, graduate students, dentists, and nurse practitioners) are faced with an enormous amount of information coming from scientific literature, computerized patient records and artificial intelligence. Methods for dealing with this avalanche of data and ways to retain focus on key patient and scientific matters are explored, and practical suggestions to improve doctor-patient interactions are included, with a focus on approaching care regarding the patient's life context and personhood. The ninety-nine lessons demonstrate how to enhance understanding of the humanity of both the patient and the doctor and how awareness of thought is essential for innovative and compassionate care and research.