Considering that the average age for diagnosis of autism spectrum disorder (ASD) is 4–5 years, testing screening methods for ASD risk in early infancy is a public health priority. This study aims to identify the risks for development of ASD in children born prematurely and hospitalized in a neonatal intensive care unit (NICU) and explore the association with pre-, peri- and postnatal factors. Methods: The children’s families were contacted by telephone when their child was between 18 and 24 months of age, to apply the Modified Checklist for Autism in Toddlers (M-CHAT). The sample consisted of 40 children (57.5% boys). M-CHAT screening revealed that 50% of the sample showed early signs of ASD. Although the frequency of delayed development was higher in boys, this difference was not statistically significant between the sexes (p = 0.11). Assessment of the association between perinatal conditions and early signs of autism in children hospitalized in an NICU exhibited no correlation between the factors analyzed (birth weight and type of delivery). The findings indicate a high risk of ASD in premature children, demonstrating no associations with gestational and neonatal variables or the hospitalization conditions of the NICUs investigated.