We compared anthropometric values, nutrient intake, the Healthy Eating Index and food variety in children with autism spectrum disorder (ASD), 20 on a gluten-free casein-free (GFCF) diet and 85 on a regular diet in Valencia (Spain) using 3-days food diaries. Those on the GFCF diet had a lower weight, body mass index, and total energy, pantothenic acid, calcium, phosphorus and sodium intake, but a higher intake of fiber, legumes, and vegetables. Further, the GFCF diet group had a better quality of fat intake, but needed supplementation with vitamin D. Randomized controlled trials are required to explore long-term effects of this diet on anthropometric and nutritional status (the focus of our study), but also behavioral symptoms, in children with ASD.