That question is really difficult to answer and one of the reasons why so many kids with autism are on special diets. Sometimes allergies are easy to get a definitive answer on because there can be clear symptoms (if your child eats almonds and then gets welts - they have an allergy). Some kiddos get allergy testing - the gold standard is called an oral food challenge which has to be conducted by a specially trained doctor. Unfortunately, this kind of test can be difficult for children, but especially kids on the spectrum. Having said that, not all allergies are that obvious. Regardless of whether it is an allergy, intolerance, or other issue - the symptoms can be similar and the response can be delayed which can make it really difficult to find the underlying cause. The best way to tease it out is to do a food diary. It can be time consuming, but will provide you with the kind of information your doctor will need to guide you through the process.  

It's never a bad idea to talk to your child's pediatrician or a nutritionist about diet, but you NEED to talk to someone if your child is very underweight or experiencing excessive weight gain. Although there is a lot of expected variation in children's hunger patterns some children with autism are so limited in what they eat that they can experience malnourishment or an eating disorder. On the other hand, obesity is a big concern for children with autism.