In the gastrointestinal tract, interstitial cells of Cajal (ICC) are located between nerve fibres and muscle cells and have a role in neuromuscular transmission and muscle contractility. Protein kinase C (PKC) is involved in modulation of muscle contractility by neurotransmitters, but it is not known if PKC has a role in ICC. There are 11 different PKC isoforms. The presence of PKC isoforms in ICC in guinea-pig gastrointestinal tract was examined using fluorescence immunohistochemistry and confocal microscopy. Segments of guinea-pig stomach, duodenum, ileum, proximal and distal colon were fixed in zambonis fixative. Frozen sections and wholemounts were incubated with anti-PKC antibodies (alpha, beta, delta, epsilon, gamma, iota, lambda, mu, theta) followed by fluorescent secondary antibody. Only PKC theta (theta) immunoreactivity was found in ICC. None of the other PKC isoforms (alpha, beta, delta, epsilon, gamma, iota, lambda, mu) localized to the ICC. PKC theta immunoreactivity was prominent in ICC located between the circular and longitudinal muscle layers (ICC-MY) in all regions except stomach and within the circular muscle (ICC-IM) in the large intestine. PKC theta was not present in ICC in the deep muscular plexus in either duodenum or ileum. PKC theta immunoreactivity was present in the cell body and proximal processes of the ICC. The cells containing PKC theta also contained cKit confirming the cells were ICC. ICC-MY in the ileum also contained the neurokinin (NK) 1 receptor. In conclusion, PKC theta is present in pacemaker ICC, but its function is not yet known. Functional studies will be needed to determine the role of this kinase in ICC. Knowing the second messenger cascades and being able to manipulate subpopulations of ICC will add to our understanding of the molecular and cell biology of ICC networks within the gastrointestinal tract and may ultimately help in understanding the aetiology of some gastrointestinal motor pathologies.