Qualitative researchers and social scientists are increasingly using the internet as a site for social research and observation. However, due to unique spatial arrangements online and new modes of social interaction, the internet brings with it a number of complex methodological issues. This paper draws on a case study titled Fan Fiction Online: Celebration or Appropriation? – a qualitative study conducted by the author in 2007 – and seeks to identify significant methodological issues which were encountered in the case study, and by other researchers attempting work of a similar nature. The methodological issues discussed in this paper are related to the following broad themes: the nature of the sample, modes of communication online, the blurring of public and private spaces, and confidentiality, consent and deception. This paper also finds that the discourse surrounding the relationship between online and offline realities may have significant implications for the role of Institutional Review Boards (IRB’s) and the consideration of renewed methodological guidelines online. It is suggested that renewed methodological guidelines be developed which address the unique research issues associated with the internet, while considering its relationship with the physical world.