Sometimes LaTeX tells you this:

LaTeX Warning: There were undefined references.

If you get this warning, you will notice some ?? in your document at places where references should be. For references to sections, tables of figures, just run pdflatex again (and check for typos). For bibliography references you need to run bibtex.

Let’s assume you are writing a LaTeX file with the name ‘report.tex’. Do the following:

> pdflatex report.tex
[...]
LaTeX Warning: Citation `Liu2010' on page 1 undefined on input line 39.
[...]
LaTeX Warning: Reference `fig:results' on page 1 undefined on input line 65.
[...]
LaTeX Warning: There were undefined references.
[...]
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
[...]
> bibtex report
[...]
> pdflatex report.tex
[...]
LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right.
[...]
> pdflatex report.tex
[...]

You need to run pdflatex again twice after calling bibtex. Twice, because layout may change and things end up somewhere else after you inserted the references.