How to compare XML files in C#?

Microsoft's XML Diff and Patch API should work nicely:

public void GenerateDiffGram(string originalFile, string finalFile,
                       XmlWriter diffGramWriter)
    {
        XmlDiff xmldiff = new XmlDiff(XmlDiffOptions.IgnoreChildOrder |
                                      XmlDiffOptions.IgnoreNamespaces |
                                      XmlDiffOptions.IgnorePrefixes);
        bool bIdentical = xmldiff.Compare(originalFile, finalFile, false, diffGramWriter);
        diffGramWriter.Close();
    }

If you need to, you can also use the Patch tool to compare the files and merge them:

public void PatchUp(string originalFile, string diffGramFile, string outputFile)
    {
        XmlDocument sourceDoc = new XmlDocument(new NameTable());
        sourceDoc.Load(originalFile);

        using (var reader = XmlReader.Create(diffGramFile))
        {
            XmlPatch xmlPatch = new XmlPatch();
            xmlPatch.Patch(sourceDoc, reader);

            using (var writer = XmlWriter.Create(outputFile))
            {
                sourceDoc.Save(writer);
                writer.Close();
            }
            reader.Close();
        }
    }

If you want just to compare XML's and you don't need to get what is difference, you can use XNode.DeepEquals Method:

var xmlTree1 = new XElement("Root",
    new XAttribute("Att1", 1),
    new XAttribute("Att2", 2),
    new XElement("Child1", 1),
    new XElement("Child2", "some content")
);
var xmlTree2 = new XElement("Root",
    new XAttribute("Att1", 1),
    new XAttribute("Att2", 2),
    new XElement("Child1", 1),
    new XElement("Child2", "some content")
);
Console.WriteLine(XNode.DeepEquals(xmlTree1, xmlTree2));

Personally, I would go with LINQ to XML. You can find a good tutorial at: http://msdn.microsoft.com/en-us/library/bb387061.aspx