The natural occurrence of fungal contamination was evaluated in stored nuts including Almond, cashew, peanuts and walnuts selected randomly from three different regions in Saudi Arabia. After initial preparation, the samples were cultured on potato dextrose agar. Sixty samples were analyzed and sixteen fungi belonging to eleven genera isolates were identified by morphological characteristics to genus level. The major genera of fungi isolated were Aspergillus, Penicillium, Fusarium, Monilia, Chaetomium, Alternaria, Rhizopus and Mucor. Mycological analyses revealed that the most frequent isolated fungi from different nuts were Aspergillus spp. Where it was Aspergillus flavus showed the highest prevalence in samples investigated followed by Aspergillus niger while Aspergillus parasiticus in the third rank.