Purpose: To determine body composition, energy availability, training load, and menstrual status in young elite endurance running athletes (ATH) over 1 year, and in a secondary analysis, to investigate how these factors differ between nonrunning controls (CON), and amenorrheic (AME) and eumenorrheic (EUM) ATH. Correlations to injury, illness, and performance were also examined. Methods: Altogether 13 ATH and 8 CON completed the Low Energy Availability in Females Questionnaire. Anthropometric, energy intake, and peak oxygen uptake assessments were made at 4 time points throughout the year: at baseline post competition season, post general preparation, post specific preparation, and post competition season the following year. Logs of physical activity, menstrual cycle, illness, and injury were kept by all participants. Performance was defined using the highest International Association of Athletics Federations points prior to and after the study. Results: ATH had significantly lower body mass (P < .008), fat percentage (P < .001), and body mass index (P < .027) compared with CON, while energy availability did not differ between ATH and CON. The Low Energy Availability in Females Questionnaire score was higher in ATH than in CON (P < .028), and 8 ATH (vs zero CON) were AME. The AME had significantly more injury days (P < .041) and ran less (P < .046) than EUM, while total annual running distance was positively related to changes in performance in ATH (r < .62, P < .043, n < 11). Conclusions: More than half of this group of runners was AME, and they were injured more and ran less than their EUM counterparts. Furthermore, only the EUM runners increased their performance over the course of the year.