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Differential diagnosis of autism spectrum disorder (ASD) is challenging, and uncertainty regarding a child’s diagnosis may result in under-identification or prolonged diagnostic pathways. The current study examined diagnostic certainty, or how sure clinicians were that their diagnosis was accurate, among 478 toddler and preschool-aged children referred for possible ASD to academic medical specialty clinics. Overall, 60 percent of diagnoses were made with complete certainty. Clinicians were more certain when positively identifying ASD than ruling it out. Children presenting with a moderate (vs high or low) level of observable ASD symptoms were less likely to have a certain diagnosis. Further, clinicians rated less diagnostic certainty for older children, those with public insurance, and those with higher IQ and adaptive behavior abilities.