Background Diaphragm dysfunction is common in intensive care unit and associated with weaning failure and mortality. Diagnosis gold standard is the transdiaphragmatic or tracheal pressure induced by magnetic phrenic nerve stimulation. However, the equipment is not commonly available and requires specific technical skills. We aimed to evaluate ultrasound guided transcutaneous phrenic nerve stimulation for daily bedside assessment of diaphragm function by targeted electrical phrenic nerve stimulation. Methods In this randomized cross-over study we compared a new method of ultrasound guided transcutaneous electrical phrenic nerve stimulation (SONOTEPS method) using a peripheral nerve stimulator, with the magnetic phrenic nerve stimulation. Intensive care unit adult patients under mechanical ventilation with a Richmond-Agitation-Sedation-Scale score of -4 or -5 were included. Each patient received the two methods of stimulation, in a randomized order. The primary outcome was the tracheal pressure (Ptrach) induced by stimulation. Results We analyzed 232 measures of Ptrach from 116 patients of whom 77 presented a diaphragm dysfunction (Ptrach < 11 cmH2O) and 50 a severe diaphragm dysfunction (Ptrach < 8 cmH2O). The Passing-Bablok regression showed no significant differences (intercept A of -0.03 [CI95:-0.83-0.52] and slope B of 0.98 [CI95:0.90-1.05]) between SONOTEPS method and magnetic stimulation which were positively correlated (R²=0.639). The mean bias was -1.08 (CI95 5.02, -7.18) cmH2O. The receiver operating curves showed an excellent performance for the diagnosis of diaphragm dysfunction and severe diaphragm dysfunction with respectively an area under curve of 0.90 (CI95 0.83-0.97) and 0.88 (CI95 0.82-0.95). This performance was not significantly affected by the body mass index or the presence of a neck catheter. Conclusions The SONOTEPS method is a simple and accurate tool for bedside assessment of diaphragm function with ultrasound guided transcutaneous phrenic nerve stimulation in sedated patients with no or minimal spontaneous respiratory activity.