Synaesthesia is a cognitive trait in which stimuli of one sensory modality are automatically and consistently experienced in conjunction with perceptions in a separate modality or processing stream. Investigations of synaesthesia may help determine the neural processing required in the generation of a conscious experience. In order to gain the most complete understanding of synaesthesia, we have applied an integrated neurophenomenological approach. In Chapter 2 we present an extended case study of spatial-form synaesthesia (SFS) phenomenology. This investigation goes significantly beyond the rudimentary accounts of provided elsewhere, and provides novel observations on inducer-concurrent relationships, suggesting that guided introspection techniques can provide neurobehaviourally relevant information. In Chapters 3-5 we investigate neural activity in grapheme-colour synaesthesia (GCS). In Chapter 3 we demonstrate that activation in colour selective areas during synaesthetic colour processing is dependent on individual differences in phenomenology, thereby reconciling previous attempts to replicate this key finding in the GCS literature. In Chapter 4 we find no evidence for trait level differences in context specific functional connectivity in GCS, however, we demonstrate that localisation of the synaesthetic concurrents modulate connectivity between colour and low-level visual areas. In 5 we replicate findings of trait level differences in resting state fronto-parietal networks, suggesting that the RFPN may be a significant network in aspects of the synaesthetic experience common to all participants. We demonstrate that localisation of concurrents also modulates resting state visual networks, whilst automaticity of concurrents modulates parietal networks. Both Chapters 4 and 5 support a model of synaesthesia in which localisation of concurrents is modulated by bottom-up connectivity, between colour and early visual areas. This thesis demonstrates that individual differences in synaesthetic phenomenology significantly impact neural activity. We propose that future investigations place emphasis on the phenomenological experience of the participant in the interpretation of neural effects.