Research on individuals severely affected by autism, including those who are minimally verbal, have intellectual disability or challenging behaviors, has become less common. The Autism Inpatient Collection (AIC) was initiated so data on this group is available to the research community. Ten studies utilizing phenotypic data from the first 350 AIC participants are presented. Greater autism severity, sleep disturbance, and psychiatric disorders are risks for hospitalization; fluently verbal youth experience more depression and oppositional symptoms; lower adaptive/coping skills are associated with increased problem behaviors; lower IQ is a risk for SIB; post-traumatic and suicidal symptoms are common; and challenging behaviors improve with specialized inpatient treatment. A new measure of emotion regulation and prescribing practices are described and future research discussed.