We discuss the diffuse emission of gamma rays and neutrinos from galaxy clusters in the viable models for structure formation in the universe. We use a self-consistent picture for cluster formation and evolution starting from a primordial density perturbation spectrum, and a realistic modelling for the distribution of the intergalactic medium which is abundantly present within galaxy clusters. We find that an evolving population of clusters can produce a fraction ∼ 0.5 ÷ 2% of the diffuse gamma-ray background (DGRB) observed by EGRET. This result is robust and is weakly dependent on the cosmological scenario and on the degree of evolution of the inter galactic medium (IGM) in distant clusters, because the bulk of the sources contributing to the DGRB is located at redshifts z ∼ < 0.2. We also found a correlation between the non-thermal, gamma-ray and the thermal X-ray emissions from these structures. Using this result, we derived a list of gamma-ray clusters observable with the next generation γ-ray detectors. Finally, we briefly discuss the possible relevance of galaxy clusters for neutrino astronomy and for very high energy particle astronomy.