The exclusive role of the medial temporal lobe in explicit memory has been questioned by several studies reporting medial temporal lobe involvement during implicit learning. Prior studies have demonstrated that hippocampal engagement is present during the implicit learning of perceptual associations, however, it is absent during learning response-related associations. Therefore, it was hypothesized that the function of the medial temporal lobe during implicit learning is related to the extraction of perceptual associations in general. While in most implicit learning tasks visual stimuli were used, the aim of the current functional magnetic resonance imaging (fMRI) study was to detect whether activations within medial temporal lobe structures are also found during implicit learning of auditory associations. In a modified version of the classical serial reaction time task, participants reacted to the presentation of five different tones. Unbeknownst to the participants, the tones were presented with an underlying sequential regularity that could be learned. To avoid an influence of response learning on acoustic associative learning, response buttons were remapped in every trial. After learning, two different tests were used to measure participants' conscious knowledge about the underlying sequence in order to assess the amount of implicit memory and to exclude participants with explicit knowledge acquired during learning. fMRI results revealed hippocampal activations for implicit learning of the acoustic sequence. When detecting a relation between implicit learning of acoustic associations and hippocampal activations, this study indicated a relation between hippocampal activations and memory formation of perceptual-based relational representation regardless of explicit knowledge. Thus, present findings suggest a general functional role for the formation of sequenced perceptual associations independent of the involvement of awareness.