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Patients with a recent diagnosis of schizophrenia and individuals receiving a diagnosis of autism spectrum disorder without accompanying intellectual impairment (ASD w/o intellectual impairment) during their adulthood share several clinical characteristics. Exploring under-investigated aspects of these two clinical conditions may shed light on their possible connection and facilitate differential diagnosis at very early stages. To this end, we explored the ability of 15 adults with a recent diagnosis of schizophrenia, 15 individuals diagnosed with ASD w/o intellectual impairment as adults, and 15 healthy adults to resolve sentence ambiguities with the use of syntactic prosody, and to decode happiness, anger, sadness, surprise, fear, and neutrality based on affective prosody. Results revealed intact perception of syntactic prosody in adults with schizophrenia, but impaired affective prosody recognition, which could be attributed, however, to emotion processing difficulties overall. On the other hand, individuals with ASD w/o intellectual impairment were impaired on prosody comprehension per se, as evidenced in the most challenging conditions, namely the subject-reading condition and the emotion of surprise. The differences in prosody comprehension ability between the two clinical conditions may serve as an indicator, among other signs, during the diagnostic evaluation.