The single most important piece of advice that I can offer you is this: Select a solid security audit standard...
or set of standards that you will audit against, and advise the auditee of the standard(s) well in advance of the audit. This ensures a level playing field and prevents the subject of the audit from crying foul when you examine something they didn't expect.
As far as overlooked information sources, I normally refer to two sources when preparing materials for a network security audit. The Center for Internet Security has a wonderful selection of security standards that can be adapted to suit the purposes of your audit. Second, the Payment Card Industry Data Security Standard (PCI DSS) offers a great set of general security requirements that can be used for any audit, even if you're not involved in credit card processing.
For more information:
- Read more about efforts to develop a common logging and audit standard.
- Learn best practices for Unix audit settings.
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