To evaluate the muscle thickness and prevalence of muscle atrophy of the biceps brachii/brachialis (BB) and quadriceps femoris (QF) in critically ill children using ultrasound (US). The prospective longitudinal study was conducted in the pediatric intensive care unit (PICU) of a tertiary hospital in southern Brazil with children and adolescents of both sexes, aged 1month to 12years, on invasive mechanical ventilation for 24h. US measurements were taken up to 24h after admission, 72h after, and weekly until discharge from the PICU. One hundred one patients were selected, of whom 97 underwent two evaluations, 68 three evaluations, and 26 four ultrasound evaluations. The median age was 6months, with 63 (62.4%) < 1year old. The most prevalent clinical diagnosis was respiratory diseases (70.3%). There was a reduction in BB thickness from 1 to 2weeks (- 0.10cm, p = 0.009) and in QF from 24h to 2weeks (- 0.20cm, p = 0.013) and 72h to 2weeks (- 0.18cm, p = 0.045). The prevalence of muscle atrophy (decrease > 10% in thickness) was 41.2% in at least one muscle group between 24 and 72h, 39.7% between 24h and 1week, and 59.3% between 24h and 2weeks. The US allows the evaluation of BB and QF muscle thickness in critically ill children, and monitoring muscles during PICU hospitalization is important. The prevalence of muscle atrophy was 30.8% in the biceps brachii and 46.2% in the quadriceps femoris at the end of 2weeks of PICU hospitalization, regardless of age and diagnosis. What is Known: • Ultrasound has emerged as a promising method, being a clinically valuable tool for bedside muscle monitoring in critical patients. • Using the ultrasound to measure the muscle thickness in adults has demonstrated good sensitivity for detecting muscle atrophy. However, this method has only been previously validated in few studies with small sample of pediatric patients. What is New: • Using the ultrasound, we observed that critically ill children experienced a loss of muscle thickness and muscle atrophy, especially during the second week of intubation. • The significant prevalence of muscle atrophy at the end of PICU hospitalization highlights the importance of ultrasound in identifying muscle loss.