Solid pseudopapillary neoplasms of the pancreas are low-grade malignancies, but their biological behavior cannot be stratified solely on the basis of histopathologic criteria. Aside from mutations in b-catenin and lack of genetic changes common to pancreatic ductal adenocarcinomas, little is known about the chromosomal alterations in solid pseudopapillary neoplasms. We applied array comparative genomic hybridization to a series of 12 patients. The average age was 31 years (range 12-52 years) with 10 female and 2 male patients. The average tumor size was 7.3 cm (range 2-24 cm) with five lesions greater than 5 cm. All cases had 'bland' cytology without significant pleomorphism or high nuclear grade, but seven cases demonstrated at least one of these potentially aggressive histopathologic features: size 45 cm, tumor necrosis, lymphovascular invasion, perineural invasion and peripancreatic invasion. Clinically, one lesion demonstrated aggressive behavior. By array comparative genomic hybridization, chromosomal losses and/or gains were identified in eight cases; five cases had multiple (five or more) alterations. The most common alterations were gains at 13q, 17q, 1q and 8q. Six of the seven cases with at least one aggressive feature had genetic alterations, while only two cases without adverse features had genetic alterations (P ¼ 0.024). The single clinically aggressive tumor exhibited seven chromosomal gains and four aggressive histopathologic features. Our study demonstrates that genetic alterations detected by array comparative genomic hybridization are common in solid pseudopapillary neoplasms of the pancreas. Additional study and longer follow-up are needed to determine if these genetic abnormalities could help predict clinical behavior in these neoplasms.