Functional medicine recognizes that illness does not occur in isolation. Similarly, sleep disorders do not occur in a vacuum because clinical imbalances that lead to illnesses may subsequently affect sleep, and sleep disruption and circadian dysregulation affect chronic disease. As a way of organizing clinical imbalances the Functional Medicine Matrix helps clinicians to examine the body systems, symptoms, and risk factors associated with a specific condition. The matrix provides an outline for the clinician to organize the patient’s clinical imbalances in biological systems, called nodes: these are defense and repair, energy, biotransformation and elimination, transport, communication, structural integrity, and assimilation. The Functional Medicine Matrix assists the clinician in organizing and prioritizing each patient’s health issues, including sleep disorders, as elicited by a thorough personal, family, social, and medical history. The matrix is a tool for organizing what seem to be disparate issues into a complete story to help the clinician gain a comprehensive perspective of the patient and subsequently facilitate discussion of complex health issues, including chronic disease and sleep disorders.