So your doctor just told you that you have atypical migraine and symptoms. But you're still confused - what's the difference between atypical migraine and "normal" migraine?
Essentially, if
your symptoms don't quite fit into the normal migraine profile, your doctor may say you have atypical migraine and symptoms. It's a tricky diagnosis. Your doctor has to be sure you don't have a disease that just looks like migraine. If you've had migraine, but the symptoms change drastically, your doctor may recommend a more careful series of tests.
Attempts have been made to classify atypical migraine types, but it's not easy because we're trying to classify something that is only named because it's outside classification. So there are really no typical symptoms. Your doctor may also classify your headache more specifically, such as atypical basilar migraine, but the same problem remains.
Typically, a migraine includes a headache on one side of the head. Nausea is common, as is a sensitivity to light and noise. But there are many symptoms when it comes to migraine disease, and no one symptoms is always there. Often if you have a migraine attack without a headache (commonly called migraine equivalent or silent migraine) it will be considered an atypical migraine. In children, you'll often see an attack with nausea and abdominal pain, but no headache. Facial pain is also a common symptom of atypical migraine.
An overall explanation of migraine symptoms can be found here. Some quick ways to diagnose migraine have been tried - if you want an overview of the basic and most common symptoms of migraine, check this page on symptoms. If your migraine attack seems to almost fit but not quite, you may have atypical migraine symptoms.
Proper diagnosis is complicated by a couple of things. First, migraine is often misdiagnosed to begin with. For example, it's often misdiagnosed as a sinus infection (actually a fairly rare condition), or even tension headache. It's important to make sure that you give your doctor as much information as possible, even if you've already been diagnosed with atypical migraine and symptoms. Family medical history, medications and herbal supplements you may be taking, unusual symptoms, even if you don't see how they relate - all these things may be helpful.
There are some treatments that seem to work better with atypical migraine and symptoms, depending on what those symptoms are. But for the most part your doctor will probably recommend treatments that are common to other types of migraine - whatever seems to closest fit your symptoms.
Sometimes it takes a lot of time and effort to really get the problem solved. If you really want to find answers, and are willing to do some investigating, I recommend the book What's Wrong With Me?, by Lynn M. Dannheisser and Dr Jerry M Rosenbaum (also available in the UK here). This book focuses on eight steps to self-diagnosis. The eight steps have helped many people with various so-called "mystery illnesses" to find the real (and often unexpected) source of their symptoms.
Far too many people are living with vague or wrong diagnoses. You can blame it on the doctor, or the system, but if there's a way you can find the answers, it may save a lifetime of problems.
References: Seattle Children's Hospital article on Cyclic Vomiting Syndrome (CVS), with info on atypical migraine and symptoms (cached); Dr Harvey Blumenthal article from 2001 Spectrum of a Migraine; Randolph W Evans' article on Migraine from MAGNUM; Cephalalgia article from 2001: Diagnosis of migraine: empirical analysis of a large clinical sample of atypical migraine (IHS 1.7) patients and proposed revision of the IHS criteria.; Cephalalgia International Classification of Migraine Disorders from 2004; The National Headache Foundation