*The following answer is based on my experience in the fields of Neuroscience, Biology, and to a lesser extent, Electrical Engineering.*

This is often an unnecessarily touchy subject amongst graduate students. To be clear: **As a graduate student, you can expect that your advisor will appear as an author on all of your papers.** He is providing your funding, your resources, and (ostensibly) is the Primary Investigator on whatever project you happen to be working on. Even if he does not contribute, you are working on *his* project, and he wrote the grant for it, not you. There may be situations where you will be the sole author of a paper you published during your graduate career, but those will be unusual circumstances, indeed.

That being said, you can read through the [Wikipedia article on the subject](http://en.wikipedia.org/wiki/Academic_authorship), which discusses conflict. [This Canadian Medical Association Journal article](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764586/?tool=pmcentrez) (thanks, [Wikipedia](http://en.wikipedia.org/wiki/Academic_authorship#cite_note-Reliability_of_disclosure_forms_of_authors.27_contributions-25)) states that authorship ordering conflicts occurred in over 60% of published papers. To help with things, there's a good chance your university has it's own authorship guidelines (e.g., [\[1\]](http://hms.harvard.edu/public/coi/policy/integritypolicy.html)[\[2\]](http://rio.msu.edu/authorshipguidelines.htm)); speak with your department.

Most importantly, speak with your advisor. Clear communication early on can help to stave off future problems, or sometimes communication will alert you to the fact that there may be future problems that you should address early on.