Co-occurrence of several mycotoxins (deoxynivalenol, zearalenone, T-2-toxin, HT-2 toxin) produced by field fungi, such as Fusarium graminearum and Fusarium culmorum, requires several analysis methods for their characterization. A reliable method for the determination of type A- and B-trichothecenes and zearalenone in cereal-based samples is presented. To achieve optimal mass spectrometric detection, electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) were compared. Best results were obtained with ESI by implementing a two-period switching for the ionization polarity. The limit of quantification differs for each individual substance within the range 1–10 ppb. Mean recoveries using a standardized clean-up procedure were in the 54–93% range.