Background: There is a lack of data regarding autism prevalence and factors associated with it in Arab Countries, especially in Lebanon. A study conducted in Beirut and Mount Lebanon governorates estimated the prevalence of Autism Spectrum Disorder (ASD) at 1.53% of children 16-48 months attending nurseries. This study aims at obtaining a total national ASD estimate and find factors associated with the disorder. Methods: The methodology used to collect data at a national level consisted of administering the Modified Checklist for Autism in Toddlers (M-CHAT) for screening and a self-administered questionnaire for associated factors. The final sample included 1,373 children aged 16-48 months. Prevalence estimates and crude and adjusted Odds Ratios (ORs) with 95% confidence intervals (95% CI) were generated. Results: ASD national prevalence is 1.48% with 95% CI (0.84, 2.12), with a 1.13 male/female ratio according to the M-CHAT. In the multivariable analysis, having an employed mother in the last year was protective against ASD (OR (95% CI): 0.36(0.14, 0.93)). Presence of delivery complications was a risk factor (3.58 (1.26, 10.15)). First/ second born and moral support during pregnancy were protective, whereas mother not having a university education and family history of mental illness were risk factors. These variables were not significant in the multivariable analysis, probably due to small numbers. Conclusion: This is the first study estimating ASD prevalence in the entire Lebanese population, a much needed step to know the magnitude of the disorder. More robust studies are needed to better understand this disorder and factors associated with it in Lebanon and the region that have distinct cultural/environmental characteristics.