In theory, Y-DNA tests are a great way to research your patrilineal ancestry. The Y chromosome is passed from father to son and is never recombined with the mother's DNA. Barring name changes and non-paternity events, the characteristics of your Y chromosome should be strongly associated with your surname.
In practice, Y-DNA tests can sometimes result in confusion rather than clarity. I recently assisted a client who was trying to identify his paternal grandfather. To that end, he had taken several autosomal DNA tests and a Y-DNA test. He was inundated with DNA matches. I used a Leeds Diagram to sort his autosomal DNA matches by grandparent, which revealed the surname of his paternal grandfather almost immediately. The client initially rejected this surname, because he had been told by that surname's Y-DNA group administrator that he was probably not a match.
There are at least four reasons why that may have occurred:
- One of his paternal ancestors may have changed the family surname.
- One of his paternal ancestors may have been adopted.
- One of his paternal ancestors may have been the result of a non-paternity event.
- That particular surname project has relatively few members and may not currently account for the genetic diversity in the community.
For that client, autosomal DNA was a more effective resource than Y-DNA. The pool of potential matches was much larger, and the matches he received were much closer. The limitation of autosomal DNA is that it is only reliable for about five generations (more or less).
If you're trying to push through a brick wall involving your fourth great-grandfather, Y-DNA may be your best bet. If you are a female, or if that great-grandfather is not on your direct paternal line, you will have to ask a direct male descendant of the ancestor in question to test for you.
Y-DNA tests are very expensive compared to autosomal DNA tests. If you're searching for a particular ancestor, as opposed to your more general ethnic origin, you should test at least 67 markers. Because Y-DNA has less variation than autosomal DNA, an exact match at 12 markers may be genealogically irrelevant.
 Immigrants often changed or simplified their names. Adopted children often took the surname of their new family. There can also be considerable spelling variation among names which were not intentionally changed.
 When the parent on the birth certificate or the baptismal record is not the biological parent, this represents a non-paternity event (NPE). The acronym is also interpreted as not-parent-expected.
 The Leeds Method of DNA Color Clustering was developed by Dana Leeds to visualize DNA matches by lineage.
 Many surnames have group Y-DNA projects which collect, sort, and analyze STR values to define shared ancestry.