Fungal infection of cereals grains is a problem of public health concern due to the possible risk of mycotoxins contamination. The present study investigated the prevalence of Fusarium species and their mycotoxins zearalenone (ZON), HT-2, T-2, deoxynivalenol (DON), 3-ac DON and 15-ac DON contamination in maize, wheat and rice samples from five agroecological zones i.e. zone-A, B, C, D and E of Khyber Pakhtunkhwa Province of Pakistan in spring (March-May), summer (June-August), autumn (September-November) and winter (December-February) seasons of the year 2015-16. In addition, different physical and chemical strategies were adopted to control Fusarium strains and their associated mycotoxins in maize, wheat and rice grains during storage. The mycological analysis indicated that maize, wheat and rice samples from zone-B in autumn season contained the highest total fungal viable counts i.e. 11.50×103, 3×103 and 0.8×103 CFUs/g, respectively whereas the lowest total fungal counts i.e. 6.50×103, 1 ×103, 0.22×103 CFUs/g, respectively were recorded in the samples from zone-D in spring season. Similar pattern of results was noted for total Fusaria counts in maize, wheat and rice samples. The analysis of maize, wheat and rice samples for the identification of mycotoxigenic Fusaria showed the presence of seven species which were F. graminearum, F. langsethiae, F. poae, F. culmorum, F. crookwellense, F. sporotrichioides and F. equiseti. The species showed significant (p<0.05) variation in their occurrence frequencies with respect to season, agroecological zone and cereal type. However, the overall dominant toxigenic Fusarium species in maize and rice was found to be F. langsethiae and that in wheat was F. graminearum. The data regarding mycotoxin contamination of maize, wheat and rice samples revealed that both the zones and seasons alone and in combination significantly (p<0.05) affected the mycotoxins contents of these cereals. The average value of ZON contents ranged from 610.40 to 1280.42 µg/kg in maize, 45.22 to 120.32 µg/kg in wheat and 40 to 45 µg/kg in rice. The HT-2 contents of maize samples ranged from 140.35 to 245.62 µg/kg; the lowest in the sample from zone-E in spring season and highest in the samples from zone-B in winter season. Similarly, the HT-2 content of wheat samples expressed that the highest content (65.46 µg/kg) was present in the samples from zone-B in autumn season whereas the lowest amount (45.18 µg/kg) was recorded in the samples from zone-E in spring season. The rice samples showed highest HT-2 content (35.23 µg/kg) in the autumn season of zone-B and the lowest (23.25 µg/kg) in the spring season of zone-E. The T-2 contents of maize ranged from 130.50 µg/kg in samples from zone-D in spring season to 530.55 µg/kg in samples from zoneB in the autumn season. The wheat samples expressed maximum T-2 contents (60.55 µg/kg) in the autumn season of zone-B and the lower most (35.24 µg/kg) was recorded in the spring season of zone-E. The rice samples generally showed little T-2 contents as compared to maize and wheat. The analysis of maize samples for DON contents showed the highest concentration (1570.48 µg/kg) in the samples of zone-B in autumn season while, the lowermost content (190.52 µg/kg) was perceived in the spring samples of zone-D. Likewise, the wheat samples showed the least DON contents (50.35 µg/kg) in the spring season of zone-C and the highest (110.15 µg/kg) in the samples from zone-B in autumn season. Similarly, rice samples from zone-B expressed the highest DON contents (40.37 µg/kg) in autumn while the lowest contents were recorded in the samples from zone-A in spring season. Data regarding 3-ac DON content of maize samples revealed that its contents were significantly (p<0.05) higher in zone-B during autumn season. The wheat samples from zone-C, D and E showed no detectable concentration of 3-ac DON whereas the samples from zone-A and B showed the contents ranging from 15.28 to 35.25 µg/kg. Similar pattern of results was noted for rice samples. The 15-ac DON contents were detected only is the samples from zone-A (maize and rice), zone-B (maize, wheat and rice) and zone-E (wheat) whereas no detectable level of it was analyzed in the samples from other zones during the four seasons of the year. The application of γ-radiation at dose rates of 5 and 10kGy on naturally contaminated maize, wheat and rice samples showed that total fungal counts, total Fusaria counts, and Fusarium mycotoxins were significantly reduced at 10kGy irradiations. Similarly, the samples of naturally contaminated maize, wheat and rice were subjected to dry heat treatment at 150 and 180°C. The total viable fungal counts and total viable Fusaria counts of all the three cereals were completely eliminated at 150 and 180 °C and the mycotoxins were substantially reduced. The control (no heat treated) maize samples contained 935.55, 308.30, 230.73, 1451.68, 362.11 and 156.71 µg/kg of ZON, T-2, HT-2, DON, 3-ac DON, and 15-ac DON mycotoxins, respectively. These mycotoxins were reduced to 186.57, 113.88, 37.51, 23.34, 37.86 and 39.87 µg/kg, respectively after heat treatment at 180°C. Similar results were noted for wheat and rice samples. Likewise, the total fungal count and total Fusaria counts were significantly affected by calcium propionate preservative, aw and storage time. The total fungal count in maize was maximum with no preservative (12.25×103CFUs/g) at 0.95 a w at 45 day of incubation period, whereas the fungal population decreased significantly to 7.2×103CFUs/g at 0.95 aw, 45day storage time and 1% calcium propionate. Similarly, the total fungal count, total Fusarium count for wheat and rice samples was also significantly controlled by calcium propionate as preservative at 1% concentration at reduced a w level. The mycotoxins ZON, HT-2, T-2, DON, 3-ac DON and 15-ac DON contents of maize, wheat and rice were significantly (p<0.05) affected by aw, storage time and preservative concentration. Generally, the concentration of all these mycotoxins in maize, wheat and rice samples increased with increasing aw level and storage time whereas a reversal of the trend was noted with increasing concentration of calcium propionate preservative. It was concluded from the study that the major cereals i.e. maize, wheat and rice of Khyber Pakhtunkhwa were contaminated with Fusarium mycotoxins whose severity was dependent on seasonal variation and geographical locations. Therefore, it is recommended to adopt suitable prevention and control measures to tackle mycotoxins contamination problem in cereals on priority basis.