Individuals with autism spectrum disorder experience a significant number of co-occurring medical conditions, yet little is known about these conditions beyond prevalence. Using large-scale de-identified medical records, we can use a novel phecode-based tool to characterize co-occurring conditions in autism spectrum disorder. We hypothesized that individuals with autism spectrum disorder experience an increased burden of co-occurring conditions as measured by presence, frequency, and duration of visits related to co-occurring conditions. Secondarily, we hypothesized that age at first encounter for autism spectrum disorder (early, <5; late, >5) would be associated with different co-occurring conditions. The International Classification of Diseases, Ninth Revision, codes were extracted from a large anonymized electronic medical center database for 3097 individuals with autism spectrum disorder and 3097 matched controls. Co-occurring conditions were characterized using a novel tool (pyPheWAS) to examine presence, frequency, and duration of each condition. We identified several categories of co-occurring conditions in autism spectrum disorder: neurological (convulsions, sleep disorders); psychiatric (anxiety disorders, adjustment/conduct disorders), as well as constipation, hearing loss, and developmental delays. Our work confirms individuals with autism spectrum disorder are under a significant medical burden, with increased duration and frequency of visits associated with co-occurring conditions. Adequate management of these conditions could improve quality of life for individuals with autism spectrum disorder.