Physical examination (PE) has always been a corner stone of medical practice. The recent advances in imaging and fading of doctors' ability in performing it, however, raised doubts on PE usefulness. Point-of-care ultrasonography (POCUS) is gaining ground in medicine with the detection of free fluids being one of its main applications. To estimate physicians' confidence and use of PE and POCUS for the detection of abdominal or pleural free fluid, we conducted a cross-sectional survey. In all, 246 internal and emergency medicine physicians answered to the survey (197 in-hospital physicians and 49 general practitioners; response rate 28.5%). Almost all declared to perform PE in case of suspected ascites or pleural effusion (88% and 90%, respectively). The highest rates of confidence were observed in conventional PE signs (91% for diminished breath sounds, 80% for dullness to thorax percussion, and 66% for abdominal flank dullness). For the remaining signs, rates of confidence were less than 53%. Physicians with > 15 years of experience and POCUS-naïve doctors reported higher confidence in PE. Most of emergency and almost half of internal medicine physicians (78% and 44%, respectively) attended a structured POCUS course. POCUS use was higher among trained physicians for both ascites (84% vs 50%, p < 0.001) and pleural effusion (80% vs 34%, p < 0.001). Similarly, higher POCUS use was observed in younger physicians. In conclusion, PE is frequently performed and rates of confidence are low for most PE signs, especially among young doctors and POCUS users. This detailed inventory suggests an ongoing shift towards POCUS integration in clinical practice.