CLN2 Batten disease is a predominantly late infantile form of neuronal ceroid lipofuscinosis. Symptoms of CLN2 disease emerge early in life typically between the ages of 2 and 4 years of age and include seizures, as well as loss of motor, language, and vision functioning. Children with CLN2 disease can present with behavioral challenges including anxiety, reduced social skills, inattention, and agitation. Additionally, 80% of children with CLN2 disease present with early language delays. Behavioral challenges and language delays are also common in children with Autism Spectrum Disorder (ASD). The present study aims to compare behavioral, developmental, and adaptive behavior data in children with CLN2 Batten disease with and without a clinical diagnosis of ASD. Data was collected as part of a current, larger, longitudinal clinical trial. Participants included 31 children (19 females) between the ages of 1-5 years with a diagnosis of CLN2 Batten disease. This sample was characterized to include children with CLN2 disease that received a clinical diagnosis of ASD (ASD; N = 11; 36%) and children without a diagnosis of ASD (No-ASD; N = 20; 64%). Statistically significant group differences across T-scores are present on CBCL scales assessing emotional reactivity (t (18) = 2.22 p <.05), anxiety (t (18) = 2.2, p <.05), attention problems (t (18) = 3.87, p <.01), and aggression (t (18) =3.0, p <.01) with children with CLN2 disease and ASD reported by caregivers to demonstrate more symptoms. Results suggest that children with CLN2 disease and ASD may be at higher risk for increased behavioral challenges such aggression, externalizing problems, anxiety, and symptoms of ADHD. Behavioral therapy should be considered to reduce behavioral challenges, enhance skill acquisition and maintenance, and improve overall quality of life for individuals with Batten disease and their families.