Visual skills, including numerosity estimation are reported to be superior in autism spectrum disorders (ASD). This phenomenon is attributed to individuals with ASD processing local features, rather than the Gestalt. We examined the neural correlates of numerosity estimation in adults with and without ASD, to disentangle perceptual atypicalities from numerosity processing. Fourteen adults with ASD and matched typically developed (TD) controls estimated the number of dots (80–150) arranged either randomly (local information) or in meaningful patterns (global information) while brain activity was recorded with magnetoencephalography (MEG). Behavioral results showed no significant group difference in the errors of estimation. However, numerical estimation in ASD was more variable across numerosities than TD and was not affected by the global arrangement of the dots. At 80–120 ms, MEG analyses revealed early significant differences (TD > ASD) in source amplitudes in visual areas, followed from 120 to 400 ms by group differences in temporal, and then parietal regions. After 400 ms, a source was found in the superior frontal gyrus in TD only. Activation in temporal areas was differently sensitive to the global arrangement of dots in TD and ASD. MEG data show that individuals with autism exhibit widespread functional abnormalities. Differences in temporal regions could be linked to atypical global perception. Occipital followed by parietal and frontal differences might be driven by abnormalities in the processing and conversion of visual input into a number-selective neural code and complex cognitive decisional stages. These results suggest overlapping atypicalities in sensory, perceptual and number-related processing during numerosity estimation in ASD. Hum Brain Mapp 35:4362–4385, 2014. © 2014 Wiley Periodicals, Inc.