Human herpesvirus 6 (HHV6) encephalitis and Wernicke’s encephalopathy are treatable yet frequently undiagnosed causes of encephalopathy in pediatric recipients of allogeneic and autologous hematopoietic cell transplantation. Here we review representative cases of both conditions to highlight specific and relevant neurologic features which prompted effective diagnosis and treatment. Two patients with confusion accompanied by seizures, memory changes, or specific visual hallucinations and HHV6 detectable by PCR in cerebrospinal fluid had improvement in viral load with ganciclovir or foscarnet treatment. Two patients had confusion, ataxia, or ocular changes and low serum thiamine levels, which resolved with parenteral thiamine. In all cases, definitive diagnosis and treatment were facilitated by a high index of suspicion and search for specific pathognomonic neurologic deficits accompanying the confusional state. It is critical to clinically differentiate these two conditions from other common neurologic syndromes occurring after transplant, allowing potentially improved patient outcomes by prompt diagnosis, and effective treatment.