As the precise functions of adjuvants become clearer, opportunities are presented in their complementary use for the induction of tailored immune responses to subunit vaccines. Here we comparatively investigate the immunological outcome following intranasal or intramuscular immunisation with Helicobacter pylori urease admixed to a chitosan and muramyl di-peptide (MDP) combination. MDP appeared to limit the antigenicity of rUre by either administration route. Nasal administration of the combined adjuvant formulation resulted in an up-regulation of type I recall responses in splenocytes as opposed to adjuvantisation with chitosan alone. In contrast, intramuscular immunisation appeared to limit the responsiveness to the antigen when adjuvanted with chitosan and even more so when chitosan was combined with MDP, suggesting that the mechanism of adjuvantisation and adjuvant synergy differed depending on the immunisation route. Recognising the benefit of improved delivery of MDP intranasally due to the specific physiological effects of chitosan, we discuss the impact of the newly identified pathogen associated molecular pattern (PAMP) role of MDP with respect to the adjuvanticity of proposed chemical variants of this peptide adjuvant.