Introduction Autism spectrum disorder (ASD) is a lifelong disorder affecting children quite early in life, manifested as delays in communication and stereotypic behaviors. To date, it is diagnosed clinically using the Diagnostic and Statistical Manual-5 (DSM-V) criteria due to the lack of biomarkers that can specifically denote the disorder. The role of synucleins in this context has been considered due to the increasing evidence of neurodegeneration in many autistic children. Synucleins are a group of soluble neuronal proteins primarily expressed in the central nervous system. They are of three types: α-, β-, and ɣ-synuclein. α-synuclein is involved in vesicle trafficking and release of neurotransmitters. There is no uniformity in the scientific community regarding their levels of autism, with few studies showing increasing levels and others to the contrary. Hence, the present study was conceived to analyze the levels of α-synuclein and β-synuclein in autistic children and to correlate with the disease severity. Objectives The main objective of the study was to assess the levels of α- and β-synuclein in autistic children of 2-8 years of age and to identify the correlation between the severity of core symptoms of autism and α- and β-synuclein levels. It is intended to assess the possibility of using α- and β-synuclein/their ratio as a biomarker of the severity of autism. Materials and methods Plasma levels of α-synuclein and β-synuclein were measured in 160 ASD children and 40 healthy age and sex-matched children by ELISA. Their symptom severity was assessed with CARS-2 ST and the Indian Scale of Autism Assessment (ISAA). Values of α- and β-synuclein were analyzed for correlation with the severity rating of ASD. Cut-off values of α-synuclein and β-synuclein that discriminate the presence of autism and its severity were assessed using Jamovi 2.4.14 software. Results The results show that α-synuclein levels were significantly reduced (5.02 ± 0.586; range: 3.13-6.0 ng/ml) when compared with healthy controls (29.47 ± 18.62 ng/ml; range: 22.39- 36.56) with p < 0.001, and β-synuclein levels were elevated (1424 ng/ml ± 122; range: 1229-1616 ng/ml) when compared to control, though not significantly. Plasma levels of α-synuclein significantly correlate with disease severity with good diagnostic accuracy (86%), but β-synuclein levels did not correlate with severity. The fold changes of synucleins, especially the fold decrease in levels of α-synuclein, were discriminative for the diagnosis and severity with good sensitivity (93.6%), specificity (74.3%), positive predictive (92.6%), and negative predictive values (76.5%). The fold increase in β-synuclein did not have any significance in predicting the severity of autism. Conclusion The present study showed that α-synuclein and β-synuclein were associated with ASD and can be used to assess its severity. A fold decrease in α-synuclein was found to have good discriminating value in differentiating the severity of autism. It may be of use especially in mild and high-functioning autism, when clinically distinguishing them may be difficult.