LIGO recently commenced its sixth science run (S6) simultaneously with Virgo starting its second science run (VSR2). Because of differing interferometer configurations with respect to S5, much effort has been invested understanding new sources of noise in the LIGO S6 interferometers. The LIGO Scientific Collaboration's detector characterization working group is actively investigating the origin of noise in the LIGO interferometers and determining the periods of good, bad or questionable data quality. We describe the instrumental issues found to affect the data quality in S6 and the vetoes developed for burst and inspiral searches. The methods used to search for and identify periodic noise lines are also presented. A summary of other noise search efforts in S6 is also given.