In recent years, the less-studied mycotoxins have attracted increasing interest due to the lack of survey data and their ability to cause toxic effects in animals and humans. To fill the gap, the aim of this three-year survey was to investigate the presence and co-occurrence of and other mycotoxins in a total of 433 cereal grain samples from Slovenian farms and agricultural cooperatives from 2014 to 2016. Using the multi-mycotoxin method, 14 mycotoxins were determined. In 53% of 433 analysed samples, contamination with at least one mycotoxin was found. Deoxynivalenol (DON) and tenuazonic acid (TeA) were present in 32% and 26% of cereal grain samples, respectively, whereas alternariol (AOH), tentoxin (TEN), alternariol monomethyl ether (AME), 3- and 15-acetyldeoxynivalenol (3- and 15-AcDON), and zearalenone (ZEN) were present in fewer than 15% of the samples. Ochratoxin A (OTA) was found in one rye sample, while diacetoxyscirpenol (DAS), HT-2 and T-2 toxin, and fumonisins B and B (FB1 and FB2) were not detected. The highest maximum and median concentrations of toxins were determined in spelt in 2016 (TeA, 2277 µg/kg and 203 µg/kg, respectively), and those of toxins in wheat in 2015 (DON, 4082 µg/kg and 387 µg/kg, respectively). The co-occurrence of two or more mycotoxins was found in 43% of the positive samples. The correlations between toxins were very weak but statistically significant (r: 0.15-0.17, : 0.0042-0.0165). A well-known correlation between toxins DON and ZEN was weak and highly significant (r = 0.28, < 0.0001).