This study provides insights into the benefits of phoneme awareness intervention for children with complex communication needs (CCN). The specific aims of the study were: (1) to determine whether phoneme awareness skills can be successfully trained in children with CCN; and (2) to observe any transfer effects to phoneme awareness tasks not directly targeted during intervention, and to the encoding and decoding of printed words. Two children participated in the study: Scott, aged 7 and Anna, aged 10. Prior to intervention, both children exhibited poor phoneme awareness knowledge and severely delayed written language skills. Scott received 7 hours of intervention that focused on improving his phoneme identity skills and his letter-sound knowledge. Anna received 11 hours of intervention that focused on improving her phoneme segmentation and manipulation skills. Results indicated that both children responded favourably to the phoneme awareness intervention, demonstrating improved performance on trained tasks compared with untrained control measures. Anna generalised phoneme segmentation skills to novel words. Both children, however, demonstrated little or no generalisation to different versions of the same tasks or to other phoneme awareness and literacy tasks. Further research is required to ascertain the extent of generalisation that is possible for children with CCN.