BACKGROUND AND PURPOSE: Children often are referred for physical therapy with the diagnosis of hypotonia when the definitive cause of hypotonia is unknown. The purpose of this case report is to describe the clinical decision-making process using the Hypothesis-Oriented Algorithm for Clinicians II (HOAC II) for an infant with hypotonia and gross motor delay. CASE DESCRIPTION: The patient was a 5-month-old infant who had been evaluated by a neurologist and then referred for physical therapy by his pediatrician. Physical therapist evaluation results and clinical observations of marked hypotonia, significant gross motor delay, tongue fasciculations, feeding difficulties, and respiratory abnormalities prompted necessary referral to specialists. Recognition of developmental, neurologic, and respiratory abnormalities facilitated clinical decision making for determining the appropriate physical therapy plan of care. OUTCOMES: During the brief episode of physical therapy care, the patient was referred to a feeding specialist and diagnosed with pharyngeal-phase dysphasia and mild aspiration. Continued global weakness, signs and symptoms of type 1 spinal muscular atrophy (SMA), and concerns about increased work of breathing and respiratory compromise were discussed with the referring physician. After inconclusive laboratory testing for metabolic etiologies of hypotonia, a genetics consult was recommended and confirmed the diagnosis of type 1 SMA at 9 months of age. DISCUSSION: Physical therapists use clinical decision making to determine whether to treat patients or to refer them to other medical professionals. Accurate and timely referral to appropriate specialists may assist families in obtaining a diagnosis for their child and guide necessary interventions. In the case of type 1 SMA, early diagnosis may affect outcomes and survival rate in this pediatric population.