Purpose: To investigate any relation of behavior problems with cranial Diffusion Tensor Imaging (DTI) and Magnetic Resonance Spectroscopy (MRS) findings in autism spectrum disorders. Materials and Methods: A total of 20 males children (12 autistic patients and 8 healthy controls) was examined by cranial DTI and MRS. The Aberrant Behavior Checklist (ABC) was used to calculate the irritability, lethargy-social withdrawal, stereotypic behavior, hyperactivity, and speech disorder scores for each patient. The results of MRS and DTI were evaluated together with the ABC scores. Results: Fractional anisotropy (FA) values demonstrated significant decreases in the left frontoparietal white matter, anterior limb of the right internal capsule, and left middle cerebellar peduncle as the behavior problem scores elevated (P < 0.05). With the exception of social withdrawal, as the behavior problem scores increased, metabolite levels increased, as well. Conclusion: The positive correlation between the MRS findings, behavior problem scores, and metabolite levels suggests the presence of a dysfunction leading to hypo and hyper neuronal function in various locations. Reduced FA values in DTI and negative correlation of behavior problems with FA values in the contralateral hemisphere, may indicate reduced myelination and abnormal axonal organization.