4 Fig. 5. The fractional difference between the combined energy spectrum of the Auger Observatory and a spectrum with an index of 2.6 [18]. Data from HiRes experiment are shown for comparison [20]. The two features – the ankle and the GZK suppression – are visible. Fig. 6. The upper limits on the fraction of photons in the in- tegral cosmic ray flux measured by previous and current ex- periments [11]. Also predictions from top-down models and predictions of the GZK photon fraction are shown. The cur- rent limit given by hybrid and surface detector data measured by the Pierre Auger Observatory already excluded majority of top-down models. $^{spectrum: the ankle at the energy of 4}$×10 18 eV and the suppression above energies one magnitude higher. The suppression is statistically very significant being at the level of more than eight standard deviations. Although it is consistent with the prediction of the GZK mechanism, effects caused by cosmic ray sources themselves cannot be yet excluded. Fluorescence detector uncertainties dominate system- atic uncertainties of the energy determination in the re- sults from the Pierre Auger Observatory. Total system- atic uncertainty is 22% at present [19]. down models of cosmic-ray origin (i.e. cosmic rays com- ing from decays of superheavy particles) and in the fu- ture it could reach the level of GZK photons (i.e pho- tons produced during interaction of UHECRs with the cosmic microwave background radiation). The corre- sponding photon fluxes are sensitive to source features (type of primary, injection spectrum, distance to sources etc.) and to propagation parameters (extragalactic radio backgrounds and magnetic fields). 5. Upper Limit on Flux of Photons Neither photons nor neutrinos were detected above the energy of ∼ 10 14 eV yet. Both of them are stable and neutral particles which are not affected by magnetic fields during their propagation in space and therefore they point back to their sources. The successful detec- tion of ultra high energy photons or neutrinos could help to solve the whole mystery of cosmic rays and lead to the discovery of point sources or indicate a need for a new physics. The detection of small flux of ultra-high energy photons could among others confirm the GZK mecha- nism. Showers initiated by UHE photons develop differently from showers induced by nuclear primaries. Particularly, observables related to the development stage of mea- sured air showers (such as the depth of shower maximum X$_{max}$ ) provide good sensitivity to identify primary pho- tons. Photon showers are expected to develop deeper in the atmosphere (larger X$_{max}$ ) than hadronic ones. Pho- ton showers also contain fewer secondary muons, since photoproduction and direct muon pair production are expected to play only a sub-dominant role. The air shower maxima can be directly observed by the fluores- cence detector. Moreover, two simple but robust observ- ables can be extracted from data measured by the surface detector. These observables provide good discrimination between photon and nuclear primaries. They are the ra- dius of curvature of the shower front and the risetime at given core distance. The Pierre Auger Observatory has the sensitivity for a detection of photons [21]. Measured upper limit on the fraction of photons in the integral cosmic-ray flux is shown in Fig. 6.. The limit ruled out many top- Up to now, no neutrino candidate has been observed in the data. The upper limit is still almost one order of magnitude above the GZK neutrino predictions. The Pierre Auger Observatory will keep taking data for about 20 years over which the bound will improve by more than an order of magnitude if no neutrino candidate is found. The neutrino detection method focuses on a search for very inclined young showers. The neutrino events would have a significant electromagnetic component leading to a broad time structure of detected signals in contrast to nucleonic-induced showers. The surface detector of the Pierre Auger Observatory has a satisfactory discrimina- tion power against the larger background of nucleonic showers over a broad angular range [23]. The Earth- skimming tau neutrinos are also expected to be observed by detecting showers induced by the decay of emerging τ leptons, after the propagation of neutrinos through the Earth [22]. There are good reasons also for the searching for ultra- high energy neutrinos. Their observation should open a new window to the universe since they can give infor- mation on regions that are otherwise hidden from ob- servation by large amounts of matter. Moreover, neutri- nos are not deviated by magnetic fields and hence they maintain the direction of their production places. The existence of ultra-high energy cosmic rays of energies ex- ceeding 10 19 eV makes it most reasonable to expect neu- trino fluxes reaching similar energies. Although the ori- gin of cosmic rays and their production mechanisms are still unknown, neutrinos are expected to be produced together with the cosmic rays and also in their inter- actions with either interstellar and intergalactic matter or the background radiation fields during propagation. Unfortunately there are still many unknowns concern- ing cosmic ray origin and neutrino fluxes remain quite uncertain. 6. Upper Limit on Flux of Neutrinos