A critical scrutiny of Freud's case the Rat Man elucidates the implications of the built-in contradictions that Freud made while evolving the psychoanalytic method. By comparing the published case of the Rat Man with Freud's private notes we get access to two different perspectives. Wishing to mould a clinical situation that would confirm his theories and uphold the image of the psychoanalyst as an authority figure, Freud was partly blind to some irrational distortions in how he perceived the interaction between the patient and himself. Contradictory explicit and unconscious “theories” and the emergence of a more modern understanding of transference, which includes inter-subjective dimensions, are expounded.